Mercurial > repos > estrain > seqsero2_v1_0_1
changeset 37:e1b40b4d1545
Uploaded
| author | estrain |
|---|---|
| date | Sat, 07 Sep 2019 15:34:01 -0400 |
| parents | 2fb62709dc5e |
| children | 758f14a0e6db |
| files | seqsero2.xml |
| diffstat | 1 files changed, 8 insertions(+), 9 deletions(-) [+] |
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--- a/seqsero2.xml Sat Sep 07 15:31:05 2019 -0400 +++ b/seqsero2.xml Sat Sep 07 15:34:01 2019 -0400 @@ -1,14 +1,13 @@ <tool id="seqsero2_v1_0_1" name="SeqSero 2 v1.0.1" version="1.0.1"> <description>Salmonella serotype prediction</description> <requirements> - <requirement type="package" version="3.6">python</requirement> - <requirement type="package" version="1.74">biopython</requirement> - <requirement type="package" version="2.7.1">blast</requirement> - <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="2.9.1">sra-tools</requirement> - <requirement type="package" version="0.7.17">bwa</requirement> - <requirement type="package" version="3.13.1">spades</requirement> - <requirement type="package" version="2.27.1">bedtools</requirement> + <requirement type="package">biopython</requirement> + <requirement type="package">blast</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">sra-tools</requirement> + <requirement type="package">bwa</requirement> + <requirement type="package">spades</requirement> + <requirement type="package">bedtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ echo "SeqSero 2 v. 1.0.1" ; @@ -36,7 +35,7 @@ ln -s $forward ${name}_1.fastq; ln -s $reverse ${name}_2.fastq; touch output/SeqSero_log.txt ; - python $__tool_directory__/SeqSero2_package.py + python3 $__tool_directory__/SeqSero2_package.py -p \${GALAXY_SLOTS:-4} -t 2 -m $mode