mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Matthias Bernt
9e48ceb169
fixes https://github.com/galaxyproject/galaxy/issues/15673 - singularity: add `--no_mount tmp` (analogous to docker's default) - do not bind `$TMPDIR:rw,$TMP:rw,$TEMP:rw` by default - instead (by default )provide a writable `/tmp` via `$_GALAXY_JOB_TMP_DIR/:/tmp:rw` note that this dir is still also available as `$_GALAXY_JOB_TMP_DIR:rw`
77 lines
2.8 KiB
XML
77 lines
2.8 KiB
XML
<tool id="mulled_example_multi_1" name="mulled_example_multi_1" version="0.1.0" license="AFL-3.0">
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<xrefs>
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<xref type="bio.tools">bedtools</xref>
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<xref type="bio.tools">samtools</xref>
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</xrefs>
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<creator>
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<person
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givenName="Björn"
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familyName="Grüning"
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url="https://github.com/bgruening"
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identifier="http://orcid.org/0000-0002-3079-6586" />
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<organization
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url="https://galaxyproject.org/iuc/"
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name="Galaxy IUC" />
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</creator>
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<requirements>
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<requirement type="package" version="1.3.1">samtools</requirement>
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<requirement type="package" version="2.26.0">bedtools</requirement>
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</requirements>
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<command><![CDATA[
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bedtools --version > '$out_file1' &&
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echo "Moo" >> '$out_file1' &&
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samtools >> '$out_file1' 2>&1 &&
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echo "Cow" >> '$out_file1' &&
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touch "\${TMP:-/tmp}/job_tmp" &&
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touch "\${TEMP:-/tmp}/job_temp" &&
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touch "\${TMPDIR:-/tmp}/job_tmpdir"
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]]></command>
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<inputs>
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<param name="input1" type="data" optional="true" />
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</inputs>
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<outputs>
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<data name="out_file1" format="txt" />
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</outputs>
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<tests>
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</tests>
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<help><![CDATA[
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This is an example mulled tool that combines bedtools and samtools in one
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command-line invocation.
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]]></help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/btq033</citation>
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<citation type="bibtex">
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@misc{SAM_def,
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title={Definition of SAM/BAM format},
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url = {https://samtools.github.io/hts-specs/},}
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</citation>
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<citation type="doi">10.1093/bioinformatics/btp352</citation>
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<citation type="doi">10.1093/bioinformatics/btr076</citation>
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<citation type="doi">10.1093/bioinformatics/btr509</citation>
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<citation type="bibtex">
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@misc{Danecek_et_al,
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Author={Danecek, P., Schiffels, S., Durbin, R.},
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title={Multiallelic calling model in bcftools (-m)},
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url = {http://samtools.github.io/bcftools/call-m.pdf},}
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</citation>
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<citation type="bibtex">
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@misc{Durbin_VCQC,
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Author={Durbin, R.},
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title={Segregation based metric for variant call QC},
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url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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</citation>
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<citation type="bibtex">
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@misc{Li_SamMath,
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Author={Li, H.},
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title={Mathematical Notes on SAMtools Algorithms},
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url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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</citation>
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<citation type="bibtex">
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@misc{SamTools_github,
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title={SAMTools GitHub page},
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url = {https://github.com/samtools/samtools},}
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</citation>
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</citations>
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</tool>
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