Mercurial > repos > iuc > hisat2
changeset 21:0b1c04a90182 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit dac38d1735c11fe614d0a986a796e33eb7f4a469
| author | iuc |
|---|---|
| date | Sat, 14 Jul 2018 09:06:59 -0400 |
| parents | 6ab42baa56e9 |
| children | a26ed87f444c |
| files | hisat2.xml |
| diffstat | 1 files changed, 11 insertions(+), 6 deletions(-) [+] |
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--- a/hisat2.xml Wed May 30 12:02:20 2018 -0400 +++ b/hisat2.xml Sat Jul 14 09:06:59 2018 -0400 @@ -1,11 +1,11 @@ -<tool id="hisat2" name="HISAT2" version="2.1.0" profile="17.01"> +<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy1" profile="17.01"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> </macros> <requirements> <requirement type="package" version="2.1.0">hisat2</requirement> - <requirement type="package" version="1.4">samtools</requirement> + <requirement type="package" version="1.8">samtools</requirement> </requirements> <stdio> <regex level="fatal" match="hisat2-align exited with value 1" source="both" /> @@ -14,9 +14,6 @@ </stdio> <version_command>hisat2 --version</version_command> <command><![CDATA[ -## Use pipefail if available to quit with first non-zero exit code -set -o | grep -q pipefail && set -o pipefail; - ## Prepare HISAT2 index #if $reference_genome.source == "history": @@ -293,8 +290,16 @@ #end if ## Convert SAM output to sorted BAM +## using the two pipe stages has the following effect +## - hisat2 and sort run in parallel, during this time sort produces +## presorted temporary files but does not produce output (hence +## view does not run) +## - once hisat is finished sort will start to merge the temporary +## files (which should be fast also on a single thread) gives the +## sorted output to view which only compresses the files (now +## using full parallelism again) -| samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}' +| samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' ## Rename any output fastq files