Mercurial > repos > nick > dunovo
changeset 10:004187820b7c draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'b133d7a65a2371efa097a11ccf123587007e1662\n'-dirty
| author | nick |
|---|---|
| date | Thu, 24 Aug 2017 01:56:34 -0400 |
| parents | 82b70a5de7ab |
| children | 134117de3cd0 |
| files | align_families.xml correct_barcodes.old.xml correct_barcodes.xml dunovo.xml make_families.xml stderr.log stdout.log tool_dependencies.xml |
| diffstat | 8 files changed, 576 insertions(+), 70 deletions(-) [+] |
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--- a/align_families.xml Thu Aug 17 12:49:49 2017 -0400 +++ b/align_families.xml Thu Aug 24 01:56:34 2017 -0400 @@ -1,12 +1,12 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="0.7.2"> +<tool id="align_families" name="Du Novo: Align families" version="0.7.6"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="0.7.5">dunovo</requirement> + <requirement type="package" version="0.7.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code">align_families.py --test --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' > '$output' + <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
--- a/correct_barcodes.old.xml Thu Aug 17 12:49:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -<?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7"> - <description>of duplex sequencing reads</description> - <requirements> - <requirement type="package" version="2.2.5">bowtie2</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="package" version="1.9">networkx</requirement> - <requirement type="package" version="0.7.1">dunovo</requirement> - <!-- TODO: require Python 2.7 --> - </requirements> - <command detect_errors="exit_code">correct-barcodes.sh -d $dist -m $mapq -p $pos '$input' > '$output' - </command> - <inputs> - <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> - <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/> - <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/> - <param name="pos" type="integer" value="2" min="0" label="Minimum start offset" help="Ignore alignments where the start positions differ by more than this."/> - </inputs> - <outputs> - <data name="output" format="tabular"/> - </outputs> - <citations> - <citation type="bibtex">@article{Stoler2016, - author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, - doi = {10.1186/s13059-016-1039-4}, - issn = {1474-760X}, - journal = {Genome biology}, - number = {1}, - pages = {180}, - pmid = {27566673}, - publisher = {Genome Biology}, - title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, - url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, - volume = {17}, - year = {2016} - }</citation> - </citations> - <help> - -**What it does** - -This is for processing duplex sequencing data. This will correct duplex barcodes and create new, larger families. Errors in barcodes normally prevent them from being recognized as the same as the other barcodes in their family. Correcting these errors allows the original, full families to be reconstructed, saving reads which would otherwise be lost. This tool accomplishes this by doing an all vs. all alignment between the barcodes with bowtie2. This identifies ones which are identical except a few, small differences. - ------ - -**Input** - -This expects the output format of the "Make families" tool. - ------ - -**Output** - -The output format is the same as the input format, ready to be consumed by the "Align families" tool. - - </help> -</tool>
--- a/correct_barcodes.xml Thu Aug 17 12:49:49 2017 -0400 +++ b/correct_barcodes.xml Thu Aug 24 01:56:34 2017 -0400 @@ -1,17 +1,17 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.2"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.6"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="2.2.5">bowtie2</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.9">networkx</requirement> - <requirement type="package" version="0.7.5">dunovo</requirement> + <requirement type="package" version="0.7.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> <command detect_errors="exit_code"><![CDATA[ baralign.sh '$input' refdir barcodes.bam && samtools view -f 256 barcodes.bam - | correct.py --test --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa + | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa | sort > '$output' ]]>
--- a/dunovo.xml Thu Aug 17 12:49:49 2017 -0400 +++ b/dunovo.xml Thu Aug 24 01:56:34 2017 -0400 @@ -1,12 +1,12 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.2"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="0.7.5">dunovo</requirement> + <requirement type="package" version="0.7.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> <command detect_errors="exit_code"><![CDATA[ - dunovo.py --test --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' + dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' #if $keep_sscs: --sscs-file sscs.fa #end if
--- a/make_families.xml Thu Aug 17 12:49:49 2017 -0400 +++ b/make_families.xml Thu Aug 24 01:56:34 2017 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="0.7.2"> +<tool id="make_families" name="Du Novo: Make families" version="0.7.6"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="0.7.5">dunovo</requirement> + <requirement type="package" version="0.7.6">dunovo</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stderr.log Thu Aug 24 01:56:34 2017 -0400 @@ -0,0 +1,87 @@ +DEBUG:galaxy.app:python path is: /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/scripts, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/plat-x86_64-linux-gnu, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-tk, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-old, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages +WARNING:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config +INFO:galaxy.config:Logging at '20' level to 'stdout' +/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + 'storage.' % (dialect.name, dialect.driver)) +/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. + 'strategies for improved performance.' % expr) +127.0.0.1 - - [24/Aug/2017:00:44:41 -0500] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:44:43 -0500] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; 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Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A51.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:03 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:04 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:04 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A01.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:06 -0500] "GET /api/tools/align_families/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:07 -0500] "GET /api/tools/align_families/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:08 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A04.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:09 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:10 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:10 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A08.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:12 -0500] "GET /api/tools/dunovo/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:12 -0500] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:14 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A10.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:16 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:19 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A14.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:23 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A19.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:27 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A23.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:31 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/54f2a3a23292eb07 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:31 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff%2C54f2a3a23292eb07&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A27.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:32 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:32 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff%2C54f2a3a23292eb07&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A31.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:34 -0500] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:37 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A33.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:38 -0500] "GET /datasets/8155e4b4bf1581ff/show_params HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:41 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A37.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:42 -0500] "GET /datasets/8155e4b4bf1581ff/stderr HTTP/1.1" 200 - "http://localhost:9090/datasets/8155e4b4bf1581ff/show_params" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:46 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A41.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:50 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A46.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:54 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A50.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:46:58 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A54.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:00 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/7b55dbb89df8f4e5 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:02 -0500] "GET /datasets/7b55dbb89df8f4e5/show_params HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:03 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=7b55dbb89df8f4e5&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A58.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:06 -0500] "GET /datasets/7b55dbb89df8f4e5/stderr HTTP/1.1" 200 - "http://localhost:9090/datasets/7b55dbb89df8f4e5/show_params" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:07 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=7b55dbb89df8f4e5&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A47%3A03.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:08 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" +127.0.0.1 - - [24/Aug/2017:00:47:08 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" + +Aborted!
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stdout.log Thu Aug 24 01:56:34 2017 -0400 @@ -0,0 +1,476 @@ +Activating virtualenv at .venv +Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages +Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) +Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) +Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied: Babel==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) +Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) +Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied: testfixtures==4.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) +Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) +Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied: requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) +Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) +Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) +Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) +Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) +Requirement already satisfied: Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied: paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) +Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) +Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) +Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) +Activating virtualenv at .venv +galaxy.queue_worker INFO 2017-08-24 00:35:46,653 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:// +galaxy.model.migrate.check INFO 2017-08-24 00:35:46,802 Migrating 127 -> 128... +galaxy.model.migrate.check INFO 2017-08-24 00:35:47,628 +galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 Migration script to add session update time (used for timeouts) +galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 +galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 +galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 Migrating 128 -> 129... +galaxy.model.migrate.check INFO 2017-08-24 00:35:48,566 +galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 Migration script to allow invalidation of job external output metadata temp files +galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 +galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 +galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 Migrating 129 -> 130... +galaxy.model.migrate.check INFO 2017-08-24 00:35:49,462 +galaxy.model.migrate.check INFO 2017-08-24 00:35:49,462 Migration script to change the 'value' column of 'user_preference' table from varchar to text. +galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 +galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 +galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 Migrating 130 -> 131... +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,375 +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 Migration script to support subworkflows and workflow request input parameters +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 Migrating 131 -> 132... +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,421 +galaxy.model.migrate.check INFO 2017-08-24 00:35:50,422 Migrating 132 -> 133... +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,403 +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 Add dependencies column to jobs table +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 Migrating 133 -> 134... +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,436 +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 Migration script to set the 'deleted' column of the +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 'history_dataset_association' table to True if 'purged' is True. +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 +galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 +galaxy.config INFO 2017-08-24 00:35:51,463 Install database targetting Galaxy's database configuration. +galaxy.visualization.genomes ERROR 2017-08-24 00:35:52,535 Error reading twobit.loc +Traceback (most recent call last): + File "/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes + for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ): +IOError: [Errno 2] No such file or directory: '/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tool-data/twobit.loc' +galaxy.util.handlers INFO 2017-08-24 00:35:52,551 Setting <handlers> default to child with id 'main' +galaxy.tools.toolbox.watcher INFO 2017-08-24 00:35:52,552 Watchdog library unavailable, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,678 Parsing the tool configuration /tmp/tmp07upmy58/tool_conf.xml +galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,708 Parsing the tool configuration /tmp/tmp07upmy58/shed_tools_conf.xml +galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,708 Parsing the tool configuration /tmp/tmp07upmy58/empty_tool_conf.xml +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,963 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,964 Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,976 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,986 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,006 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,015 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,017 Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,020 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,021 Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,254 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,256 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,257 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,257 VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,258 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,258 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,259 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,260 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,261 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,262 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2017-08-24 00:35:53,302 Loaded tour 'core.history' +galaxy.tours INFO 2017-08-24 00:35:53,352 Loaded tour 'core.galaxy_ui' +galaxy.tours INFO 2017-08-24 00:35:53,370 Loaded tour 'core.scratchbook' +galaxy.webhooks WARNING 2017-08-24 00:35:53,370 directory not found: /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config +galaxy.jobs INFO 2017-08-24 00:35:53,374 Handler 'main' will load all configured runner plugins +galaxy.jobs.handler INFO 2017-08-24 00:35:53,377 job handler stop queue started +galaxy.jobs.handler INFO 2017-08-24 00:35:53,397 job handler queue started +galaxy.app INFO 2017-08-24 00:35:53,417 Galaxy app startup finished (6932.671 ms) +galaxy.queue_worker INFO 2017-08-24 00:35:54,390 Binding and starting galaxy control worker for main +Starting server in PID 1730. +serving on http://127.0.0.1:9090 +galaxy.tools.actions.upload_common INFO 2017-08-24 00:45:06,455 tool upload1 created job id 1 +galaxy.jobs.handler INFO 2017-08-24 00:45:07,438 (1) Job dispatched +galaxy.tools.actions.upload_common INFO 2017-08-24 00:45:08,061 tool upload1 created job id 2 +galaxy.jobs.handler INFO 2017-08-24 00:45:08,599 (2) Job dispatched +Fetching package metadata ....Fetching package metadata ......................... +.Solving package specifications: . +......... + +Package plan for installation in environment /home/me/miniconda3/envs/__samtools@1.3.1: + +The following NEW packages will be INSTALLED: + + curl: 7.54.1-0 + krb5: 1.13.2-0 + libgcc: 5.2.0-0 + libssh2: 1.8.0-0 + openssl: 1.0.2l-0 + samtools: 1.3.1-5 bioconda + zlib: 1.2.11-0 + +Linking packages ... +[ ]| | 0% [krb5 ]| | 0% [libgcc ]|####### | 14% [openssl ]|############## | 28% [zlib ]|##################### | 42% [libssh2 ]|############################ | 57% [curl ]|################################### | 71% [samtools ]|########################################## | 85% [ COMPLETE ]|##################################################| 100% +# +# To activate this environment, use: +# > source activate __samtools@1.3.1 +# +# To deactivate this environment, use: +# > source deactivate __samtools@1.3.1 +# + +Solving package specifications: .....galaxy.jobs.command_factory INFO 2017-08-24 00:45:23,721 Built script [/tmp/tmp07upmy58/job_working_directory/000/1/tool_script.sh] for tool command [export PATH=$PATH:'/home/me/miniconda3/envs/__samtools@1.3.1/bin' ; python /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tools/data_source/upload.py /home/me/annex/Work/PSU/Nekrutenko/code/galaxy /tmp/tmp07upmy58/tmp/tmpH5Wi0b /tmp/tmp07upmy58/tmp/tmpzTbkTw 1:/tmp/tmp07upmy58/job_working_directory/000/1/dataset_1_files:/tmp/tmp07upmy58/files/000/dataset_1.dat] +..... + +Package plan for installation in environment /home/me/miniconda3/envs/__samtools@1.3.1: + +The following NEW packages will be INSTALLED: + + curl: 7.54.1-0 + krb5: 1.13.2-0 + libgcc: 5.2.0-0 + libssh2: 1.8.0-0 + openssl: 1.0.2l-0 + samtools: 1.3.1-5 bioconda + zlib: 1.2.11-0 + +Linking packages ... +[ ]| | 0% [krb5 ]| | 0% [libgcc ]|####### | 14% [openssl ]|############## | 28% [zlib ]|##################### | 42% [libssh2 ]|############################ | 57% [curl ]|################################### | 71% [samtools ]|########################################## | 85% [ COMPLETE ]|##################################################| 100% +# +# To activate this environment, use: +# > source activate __samtools@1.3.1 +# +# To deactivate this environment, use: +# > source deactivate __samtools@1.3.1 +# + +galaxy.jobs.command_factory INFO 2017-08-24 00:45:25,065 Built script [/tmp/tmp07upmy58/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/me/miniconda3/envs/__samtools@1.3.1/bin' ; python /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tools/data_source/upload.py /home/me/annex/Work/PSU/Nekrutenko/code/galaxy /tmp/tmp07upmy58/tmp/tmpH5Wi0b /tmp/tmp07upmy58/tmp/tmpPyOeqY 2:/tmp/tmp07upmy58/job_working_directory/000/2/dataset_2_files:/tmp/tmp07upmy58/files/000/dataset_2.dat] +galaxy.tools.actions INFO 2017-08-24 00:45:38,032 Handled output named output for tool make_families (66.517 ms) +galaxy.tools.actions INFO 2017-08-24 00:45:38,085 Added output datasets to history (53.548 ms) +galaxy.tools.actions INFO 2017-08-24 00:45:38,226 Verified access to datasets for Job[unflushed,tool_id=make_families] (44.432 ms) +galaxy.tools.actions INFO 2017-08-24 00:45:38,227 Setup for job Job[unflushed,tool_id=make_families] complete, ready to flush (141.180 ms) +galaxy.tools.actions INFO 2017-08-24 00:45:38,272 Flushed transaction for job Job[id=3,tool_id=make_families] (44.434 ms) +galaxy.jobs.handler INFO 2017-08-24 00:45:38,638 (3) Job dispatched +Fetching package metadata ............... +Solving package specifications: .......... + +Package plan for installation in environment /home/me/miniconda3/envs/__dunovo@0.7.6: + +The following packages will be downloaded: + + package | build + ---------------------------|----------------- + dunovo-0.7.6 | py27_1 93 KB bioconda + +The following NEW packages will be INSTALLED: + + bowtie2: 2.2.5-py27_2 bioconda + decorator: 4.1.2-py27_0 + dunovo: 0.7.6-py27_1 bioconda + gawk: 4.1.3-1 bioconda + gmp: 6.1.0-0 + libgcc: 5.2.0-0 + mafft: 7.221-0 bioconda + mpfr: 3.1.5-0 + networkx: 1.11-py27_0 + openssl: 1.0.2l-0 + paste: 1.7.5.1-py27_0 + perl: 5.22.0.1-0 conda-forge + perl-threaded: 5.22.0-pl5.22.0_12 bioconda + pip: 9.0.1-py27_1 + python: 2.7.13-0 + readline: 6.2-2 + samtools: 0.1.18-0 bioconda + setuptools: 27.2.0-py27_0 + sqlite: 3.13.0-0 + tk: 8.5.18-0 + wheel: 0.29.0-py27_0 + zlib: 1.2.11-0 + +Fetching packages ... +dunovo-0.7.6-p 0% | | ETA: --:--:-- 0.00 B/s dunovo-0.7.6-p 17% |##### | ETA: 0:00:00 195.57 kB/s dunovo-0.7.6-p 34% |########## | ETA: 0:00:00 196.41 kB/s dunovo-0.7.6-p 51% |################ | ETA: 0:00:00 193.80 kB/s dunovo-0.7.6-p 69% |##################### | ETA: 0:00:00 245.93 kB/s dunovo-0.7.6-p 86% |########################## | ETA: 0:00:00 231.86 kB/s dunovo-0.7.6-p 100% |###############################| ETA: 0:00:00 267.10 kB/s dunovo-0.7.6-p 100% |###############################| Time: 0:00:00 266.82 kB/s +Extracting packages ... +[ ]| | 0% [dunovo ]| | 0% [ COMPLETE ]|##################################################| 100% +Linking packages ... +[ COMPLETE ]| | 0% [gmp ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% +# +# To activate this environment, use: +# > source activate __dunovo@0.7.6 +# +# To deactivate this environment, use: +# > source deactivate __dunovo@0.7.6 +# + +galaxy.jobs.command_factory INFO 2017-08-24 00:45:51,239 Built script [/tmp/tmp07upmy58/job_working_directory/000/3/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/__dunovo@0.7.6" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/__dunovo@0.7.6' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; make-families.sh -t 12 -i 5 '/tmp/tmp07upmy58/files/000/dataset_1.dat' '/tmp/tmp07upmy58/files/000/dataset_2.dat' > '/tmp/tmp07upmy58/files/000/dataset_3.dat'] +galaxy.tools.actions INFO 2017-08-24 00:46:03,656 Handled output named output for tool correct_barcodes (40.340 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:03,694 Added output datasets to history (37.250 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:03,742 Verified access to datasets for Job[unflushed,tool_id=correct_barcodes] (17.873 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:03,743 Setup for job Job[unflushed,tool_id=correct_barcodes] complete, ready to flush (49.015 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:03,784 Flushed transaction for job Job[id=4,tool_id=correct_barcodes] (40.814 ms) +galaxy.jobs.handler INFO 2017-08-24 00:46:04,804 (4) Job dispatched +Fetching package metadata ............galaxy.tools.actions INFO 2017-08-24 00:46:10,065 Handled output named output for tool align_families (56.555 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:10,105 Added output datasets to history (39.822 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:10,192 Verified access to datasets for Job[unflushed,tool_id=align_families] (37.500 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:10,195 Setup for job Job[unflushed,tool_id=align_families] complete, ready to flush (88.615 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:10,237 Flushed transaction for job Job[id=5,tool_id=align_families] (41.788 ms) +... +Solving package specifications: .......... + +Package plan for installation in environment /home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963: + +The following NEW packages will be INSTALLED: + + bowtie2: 2.2.5-py27_2 bioconda + decorator: 4.1.2-py27_0 + dunovo: 0.7.6-py27_1 bioconda + gawk: 4.1.3-1 bioconda + gmp: 6.1.0-0 + libgcc: 5.2.0-0 + mafft: 7.221-0 bioconda + mpfr: 3.1.5-0 + networkx: 1.9.1-py27_0 + openssl: 1.0.2l-0 + paste: 1.7.5.1-py27_0 + perl: 5.22.0.1-0 conda-forge + perl-threaded: 5.22.0-pl5.22.0_12 bioconda + pip: 9.0.1-py27_1 + python: 2.7.13-0 + readline: 6.2-2 + samtools: 0.1.18-0 bioconda + setuptools: 27.2.0-py27_0 + sqlite: 3.13.0-0 + tk: 8.5.18-0 + wheel: 0.29.0-py27_0 + zlib: 1.2.11-0 + +Linking packages ... +[ ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% +# +# To activate this environment, use: +# > source activate mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963 +# +# To deactivate this environment, use: +# > source deactivate mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963 +# + +galaxy.jobs.command_factory INFO 2017-08-24 00:46:16,539 Built script [/tmp/tmp07upmy58/job_working_directory/000/4/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; baralign.sh '/tmp/tmp07upmy58/files/000/dataset_3.dat' refdir barcodes.bam && samtools view -f 256 barcodes.bam | correct.py --test --galaxy --phone-home -d 1 -m 20 -p 2 '/tmp/tmp07upmy58/files/000/dataset_3.dat' refdir/barcodes.fa | sort > '/tmp/tmp07upmy58/files/000/dataset_4.dat'] +galaxy.tools.actions INFO 2017-08-24 00:46:17,240 Handled output named dcs1 for tool dunovo (147.411 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,371 Handled output named dcs2 for tool dunovo (130.913 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,434 Handled output named sscs1 for tool dunovo (61.859 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,503 Handled output named sscs2 for tool dunovo (68.277 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,535 Added output datasets to history (32.005 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,593 Verified access to datasets for Job[unflushed,tool_id=dunovo] (20.434 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,595 Setup for job Job[unflushed,tool_id=dunovo] complete, ready to flush (59.546 ms) +galaxy.tools.actions INFO 2017-08-24 00:46:17,647 Flushed transaction for job Job[id=6,tool_id=dunovo] (51.808 ms) +galaxy.jobs.handler INFO 2017-08-24 00:46:33,411 (5) Job dispatched +Fetching package metadata ............... +Solving package specifications: .......... + +Package plan for installation in environment /home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6: + +The following NEW packages will be INSTALLED: + + bowtie2: 2.2.5-py27_2 bioconda + decorator: 4.1.2-py27_0 + dunovo: 0.7.6-py27_1 bioconda + gawk: 4.1.3-1 bioconda + gmp: 6.1.0-0 + libgcc: 5.2.0-0 + mafft: 7.221-0 bioconda + mpfr: 3.1.5-0 + networkx: 1.11-py27_0 + openssl: 1.0.2l-0 + paste: 1.7.5.1-py27_0 + perl: 5.22.0.1-0 conda-forge + perl-threaded: 5.22.0-pl5.22.0_12 bioconda + pip: 9.0.1-py27_1 + python: 2.7.13-0 + readline: 6.2-2 + samtools: 0.1.18-0 bioconda + setuptools: 27.2.0-py27_0 + sqlite: 3.13.0-0 + tk: 8.5.18-0 + wheel: 0.29.0-py27_0 + zlib: 1.2.11-0 + +Linking packages ... +[ ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% +# +# To activate this environment, use: +# > source activate mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6 +# +# To deactivate this environment, use: +# > source deactivate mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6 +# + +galaxy.jobs.command_factory INFO 2017-08-24 00:46:45,677 Built script [/tmp/tmp07upmy58/job_working_directory/000/5/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; align_families.py --test --galaxy --phone-home -p ${GALAXY_SLOTS:-1} '/tmp/tmp07upmy58/files/000/dataset_4.dat' > '/tmp/tmp07upmy58/files/000/dataset_5.dat'] +galaxy.jobs.handler INFO 2017-08-24 00:46:56,416 (6) Job dispatched +galaxy.jobs.command_factory INFO 2017-08-24 00:46:56,858 Built script [/tmp/tmp07upmy58/job_working_directory/000/6/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/__dunovo@0.7.6" ] || +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/__dunovo@0.7.6' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done ; dunovo.py --test --galaxy --phone-home -r 3 -q 25 -F sanger '/tmp/tmp07upmy58/files/000/dataset_5.dat' --sscs-file sscs.fa > duplex.fa && outconv.py duplex.fa -1 '/tmp/tmp07upmy58/files/000/dataset_6.dat' -2 '/tmp/tmp07upmy58/files/000/dataset_7.dat' && outconv.py sscs.fa -1 '/tmp/tmp07upmy58/files/000/dataset_8.dat' -2 '/tmp/tmp07upmy58/files/000/dataset_9.dat'] +Starting subprocess with file monitor +^C caught in monitor process +[31mplanemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.[0m +[32m[1mStarting galaxy with command [cd /home/me/bx/code/galaxy; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/me/annex/Work/PSU/Nekrutenko/code/duplex/.venv/bin/virtualenv -p /usr/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /home/me/bx/code/galaxy/run.sh $COMMON_STARTUP_ARGS --server-name 'planemo99092' --reload][0m
--- a/tool_dependencies.xml Thu Aug 17 12:49:49 2017 -0400 +++ b/tool_dependencies.xml Thu Aug 24 01:56:34 2017 -0400 @@ -12,10 +12,10 @@ <package name="networkx" version="1.9"> <repository changeset_revision="2ca57555a756" name="package_networkx_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="dunovo" version="0.7.5"> + <package name="dunovo" version="0.7.6"> <install version="1.0"> <actions> - <action sha256sum="76f6c54d4a79d9c0d2abe3efd4c23d9ba496debb3087cafecaec53fe8879474b" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.5.tar.gz</action> + <action sha256sum="d184d192f7b7577826c240ee8f0488046b0b38e032325dcf9aa3f6c730f8ea0d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.6.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory>