Mercurial > repos > chrisw > monorail_test
changeset 5:d2d9937d1f9c draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 12 Feb 2019 13:51:52 -0500 |
| parents | ae546ad6f2f4 |
| children | 4104eb494bf8 |
| files | .shed.yml monorail.sh monorail.xml tool_dependencies.xml |
| diffstat | 4 files changed, 18 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Feb 12 13:51:52 2019 -0500 @@ -0,0 +1,10 @@ +categories: + - RNA +description: Monorail is a RNA-seq analysis which produces coverage & junction summaries +long_description: | + Monorail is a RNA-seq analysis pipeline which produces summarized coverage and junction information w/o the cost of keeping BAMs. + It runs STAR, samtools, and bamcount at its core to produce its results efficiently. +name: monorail +owner: ChristopherWilks +remote_repository_url: https://github.com/ChristopherWilks/monorail_galaxy +type: unrestricted
--- a/monorail.sh Tue Feb 12 11:56:25 2019 -0500 +++ b/monorail.sh Tue Feb 12 13:51:52 2019 -0500 @@ -29,4 +29,4 @@ samtools index -@ $threads $sorted_bam >> stools.log 2>&1 #get coverage summaries -bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1 +bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc > bc.log 2>&1
--- a/monorail.xml Tue Feb 12 11:56:25 2019 -0500 +++ b/monorail.xml Tue Feb 12 13:51:52 2019 -0500 @@ -2,6 +2,7 @@ <requirements> <requirement type="package" version="1.9">samtools</requirement> <requirement type="package" version="2.6.0b">star</requirement> + <requirement type="package" version="0.2.6">bamcount</requirement> <!-- <requirement type="package" version="5.4.0">snakemake-minimal</requirement> --> </requirements> <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 12 13:51:52 2019 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bamcount" version="0.2.6"> + <repository changeset_revision="f02b4483eda2" name="bamcount_test" owner="chrisw" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>