Mercurial > repos > charles > bismark_upgrade_proposition
changeset 1:76faf71cc0b8 draft
Uploaded
| author | charles |
|---|---|
| date | Mon, 07 Nov 2016 03:35:59 -0500 |
| parents | 18858b9321de |
| children | 2492ef09c164 |
| files | bismark/tool-data/all_fasta.loc.sample bismark/tool-data/bismark_indexes.loc.sample bismark/tool-data/bowtie2_indices.loc.sample bismark/tool-data/bowtie_indices.loc.sample |
| diffstat | 4 files changed, 21 insertions(+), 74 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark/tool-data/all_fasta.loc.sample Mon Nov 07 03:35:59 2016 -0500 @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +#Arabidopsis_thaliana Arabidopsis_thaliana_TAIR10 Arabidopsis_thaliana: TAIR 10 /export/home1/users/biocomp/chbernar/galaxy_testing/tool-data/from_personal_data/Fasta/TAIR10.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark/tool-data/bismark_indexes.loc.sample Mon Nov 07 03:35:59 2016 -0500 @@ -0,0 +1,2 @@ +#<species> <version> <release> <value> <dbkey> <name> <path> +#Arabidopsis_thaliana TAIR10 30 Arabidopsis_t_TAIR10_30 Arabidopsis_t_TAIR10_30 Arabidopsis thaliana: TAIR10 /export/home1/users/biocomp/chbernar/galaxy_testing/tool-data/from_personal_data/bismark_indexes/Arabidopsis_thaliana_TAIR10/Bisulfite_Genome \ No newline at end of file
--- a/bismark/tool-data/bowtie2_indices.loc.sample Mon Nov 07 03:31:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie2 indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie2/hg18/, -#then the bowtie2_indices.loc entry would look like this: -# -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 -# -#and your /depot/data2/galaxy/bowtie2/hg18/ directory -#would contain hg18.*.ebwt files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... -# -#Your bowtie2_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 -#...etc... -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. -#
--- a/bismark/tool-data/bowtie_indices.loc.sample Mon Nov 07 03:31:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie_indices.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, -#then the bowtie_indices.loc entry would look like this: -# -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -# -#and your /depot/data2/galaxy/bowtie/hg18/ directory -#would contain hg18.*.ebwt files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... -# -#Your bowtie_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 -#...etc... -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. -#