Mercurial > repos > eduardo > download_and_align
changeset 20:083c25559b6b
updated cutadapt dependency to 1.8 to solve env problem
| author | Eduardo <eduardoalves@abdn.ac.uk> |
|---|---|
| date | Tue, 04 Aug 2015 12:01:09 +0100 |
| parents | d839829f8494 |
| children | 92b1945d1f64 d4b97324deb3 |
| files | download_align.xml tool_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 6 deletions(-) [+] |
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--- a/download_align.xml Mon Aug 03 17:32:31 2015 +0100 +++ b/download_align.xml Tue Aug 04 12:01:09 2015 +0100 @@ -1,14 +1,14 @@ <tool id="download_align" name="Download and align" version="0.0.1"> <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description> <requirements> - <requirement type="package" version="1.6">cutadapt</requirement> + <requirement type="package" version="1.8">cutadapt</requirement> <requirement type="package" version="2.2.4">bowtie2</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <command> #set index_path = '' #if str($reference_genome.source) == "history": - echo \${PATH} && bowtie2-build "$reference_genome.own_file" genome && + bowtie2-build "$reference_genome.own_file" genome && ln -s "$reference_genome.own_file" genome.fa && #set index_path = 'genome' #else:
--- a/tool_dependencies.xml Mon Aug 03 17:32:31 2015 +0100 +++ b/tool_dependencies.xml Tue Aug 04 12:01:09 2015 +0100 @@ -6,11 +6,9 @@ <package name="samtools" version="0.1.18"> <repository name="package_samtools_0_1_18" owner="devteam" /> </package> - <package name="cutadapt" version="1.6"> - <repository name="package_cutadapt_1_6" owner="lparsons" /> + <package name="cutadapt" version="1.8"> + <repository name="package_cutadapt_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> </package> </tool_dependency> -<tool_dependency> -