[med-svn] [Git][med-team/malt][master] 4 commits: Providing manpages
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Fri Jan 21 20:29:05 GMT 2022
Pierre Gruet pushed to branch master at Debian Med / malt
Commits:
b09207b9 by Pierre Gruet at 2022-01-21T21:19:09+01:00
Providing manpages
- - - - -
95c3ccff by Pierre Gruet at 2022-01-21T21:22:47+01:00
Revising short description
- - - - -
096a25aa by Pierre Gruet at 2022-01-21T21:28:10+01:00
Adding ITP bug number
- - - - -
ae0376d4 by Pierre Gruet at 2022-01-21T21:28:37+01:00
Add missing build dependency on dh addon.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
- - - - -
8 changed files:
- + debian/bin/malt-build
- + debian/bin/malt-run
- debian/changelog
- debian/control
- + debian/malt.install
- + debian/malt.manpages
- + debian/manpages/malt-build.1
- + debian/manpages/malt-run.1
Changes:
=====================================
debian/bin/malt-build
=====================================
@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e
+
+# The upstream website recommends to launch malt by running 'ant run'.
+# We launch the software by calling java with the args in antbuild/build.xml.
+
+java -Xshare:off -server -Xmx4G -Duser.language=en -Duser.region=US -cp /usr/share/java/malt.jar malt.MaltBuild "$@"
=====================================
debian/bin/malt-run
=====================================
@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e
+
+# The upstream website recommends to launch malt by running 'ant run'.
+# We launch the software by calling java with the args in antbuild/build.xml.
+
+java -Xshare:off -server -Xmx4G -Duser.language=en -Duser.region=US -cp /usr/share/java/malt.jar malt.MaltRun "$@"
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-malt (0.0+git20180707.42b5cfd-1) UNRELEASED; urgency=medium
+malt (0.5.2-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #1004152)
- -- Andreas Tille <tille at debian.org> Tue, 11 Oct 2016 20:08:16 +0200
+ -- Pierre Gruet <pgt at debian.org> Fri, 21 Jan 2022 21:25:31 +0100
=====================================
debian/control
=====================================
@@ -9,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),
default-jdk,
ant,
libjloda-java (>= 0.0+git20180523),
- megan-ce
+ megan-ce,
+ debhelper
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/malt
Vcs-Git: https://salsa.debian.org/med-team/malt.git
@@ -20,7 +21,7 @@ Package: malt
Architecture: all
Depends: ${java:Depends},
${misc:Depends}
-Description: MEGAN alignment tool
+Description: sequence alignment and analysis tool to process sequencing data
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and
analysis tool designed for processing high-throughput sequencing data,
especially in the context of metagenomics. It is an extension of MEGAN6,
=====================================
debian/malt.install
=====================================
@@ -0,0 +1,2 @@
+debian/bin/malt-build usr/bin
+debian/bin/malt-run usr/bin
=====================================
debian/malt.manpages
=====================================
@@ -0,0 +1,2 @@
+debian/manpages/malt-build.1
+debian/manpages/malt-run.1
=====================================
debian/manpages/malt-build.1
=====================================
@@ -0,0 +1,125 @@
+.TH MALT-BUILD "1" "January 2022" "malt-build" "User Commands"
+.SH NAME
+malt-build \- Index builder for MALT (MEGAN alignment tool)
+.SH DESCRIPTION
+SYNOPSIS
+.IP
+malt-build [options]
+.PP
+DESCRIPTION
+.IP
+BUilds an index for MALT (MEGAN alignment tool)
+.PP
+OPTIONS
+.IP
+Input:
+.TP
+\fB\-i\fR, \fB\-\-input\fR [string(s)]
+Input reference file(s). Mandatory option.
+.TP
+\fB\-s\fR, \fB\-\-sequenceType\fR [string]
+Sequence type. Mandatory option. Legal values: DNA, Protein
+.IP
+Output:
+.TP
+\fB\-d\fR, \fB\-\-index\fR [string]
+Name of index directory. Mandatory option.
+.IP
+Performance:
+.TP
+\fB\-t\fR, \fB\-\-threads\fR [number]
+Number of worker threads. Default value: 8.
+.TP
+\fB\-st\fR, \fB\-\-step\fR [number]
+Step size to advance seed, values greater than 1 reduce index size and sensitivity. Default value: 1.
+.IP
+Seed:
+.TP
+\fB\-ss\fR, \fB\-\-shapes\fR [string(s)]
+Seed shape(s). Default value(s): default.
+.TP
+\fB\-mh\fR, \fB\-\-maxHitsPerSeed\fR [number]
+Maximum number of hits per seed. Default value: 1000.
+.TP
+\fB\-pr\fR, \fB\-\-proteinReduct\fR [string]
+Name or definition of protein alphabet reduction (BLOSUM50_10,BLOSUM50_11,BLOSUM50_15,BLOSUM50_4,BLOSUM50_8,DIAMOND_11,GBMR4,HSDM17,MALT_10,SDM12,UNREDUCED). Default value: DIAMOND_11.
+.IP
+Classification:
+.TP
+\fB\-c\fR, \fB\-\-classify\fR [string(s)]
+Classifications (any of EGGNOG INTERPRO2GO KEGG SEED Taxonomy). Mandatory option.
+.TP
+\fB\-g2eggnog\fR, \fB\-\-gi2eggnog\fR [string]
+GI-to-EGGNOG mapping file.
+.TP
+\fB\-r2eggnog\fR, \fB\-\-ref2eggnog\fR [string]
+RefSeq-to-EGGNOG mapping file.
+.TP
+\fB\-s2eggnog\fR, \fB\-\-syn2eggnog\fR [string]
+Synonyms-to-EGGNOG mapping file.
+.TP
+\fB\-g2interpro2go\fR, \fB\-\-gi2interpro2go\fR [string]
+GI-to-INTERPRO2GO mapping file.
+.TP
+\fB\-r2interpro2go\fR, \fB\-\-ref2interpro2go\fR [string]
+RefSeq-to-INTERPRO2GO mapping file.
+.TP
+\fB\-s2interpro2go\fR, \fB\-\-syn2interpro2go\fR [string]
+Synonyms-to-INTERPRO2GO mapping file.
+.TP
+\fB\-g2kegg\fR, \fB\-\-gi2kegg\fR [string]
+GI-to-KEGG mapping file.
+.TP
+\fB\-r2kegg\fR, \fB\-\-ref2kegg\fR [string]
+RefSeq-to-KEGG mapping file.
+.TP
+\fB\-s2kegg\fR, \fB\-\-syn2kegg\fR [string]
+Synonyms-to-KEGG mapping file.
+.TP
+\fB\-g2seed\fR, \fB\-\-gi2seed\fR [string]
+GI-to-SEED mapping file.
+.TP
+\fB\-r2seed\fR, \fB\-\-ref2seed\fR [string]
+RefSeq-to-SEED mapping file.
+.TP
+\fB\-s2seed\fR, \fB\-\-syn2seed\fR [string]
+Synonyms-to-SEED mapping file.
+.TP
+\fB\-g2taxonomy\fR, \fB\-\-gi2taxonomy\fR [string]
+GI-to-Taxonomy mapping file.
+.TP
+\fB\-r2taxonomy\fR, \fB\-\-ref2taxonomy\fR [string]
+RefSeq-to-Taxonomy mapping file.
+.TP
+\fB\-s2taxonomy\fR, \fB\-\-syn2taxonomy\fR [string]
+Synonyms-to-Taxonomy mapping file.
+.TP
+\fB\-tn\fR, \fB\-\-parseTaxonNames\fR
+Parse taxon names. Default value: true
+.TP
+\fB\-gif\fR, \fB\-\-geneInfoFile\fR [string]
+File containing gene information
+.IP
+Other:
+.TP
+\fB\-fwo\fR, \fB\-\-firstWordOnly\fR
+Save only first word of reference header. Default value: false.
+.TP
+\fB\-rns\fR, \fB\-\-random\fR [number]
+Random number generator seed. Default value: 666.
+.TP
+\fB\-hsf\fR, \fB\-\-hashScaleFactor\fR [number]
+Hash table scale factor. Default falue: 0.9.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Echo commandline options and be verbose. Default value: false.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show program usage and quit.
+.SH
+AUTHOR(s)
+.IP
+Daniel H. Huson.
+.PP
+.SH SEE ALSO
+.BR malt-run (1)
=====================================
debian/manpages/malt-run.1
=====================================
@@ -0,0 +1,194 @@
+.TH MALT-RUN "1" "January 2022" "malt-run" "User Commands"
+.SH NAME
+malt-run \- Sequences aligner using MALT (MEGAN alignment tool)
+.SH DESCRIPTION
+SYNOPSIS
+.IP
+malt-run [options]
+.PP
+DESCRIPTION
+.IP
+Aligns sequences using MALT (MEGAN alignment tool)
+.PP
+OPTIONS
+.IP
+Mode:
+.TP
+\fB\-m\fR, \fB\-\-mode\fR [string]
+Program mode. Mandatory option. Legal values: Unknown, BlastN, BlastP, BlastX, Classifier
+.TP
+\fB\-at\fR, \fB\-\-alignmentType\fR [string]
+Type of alignment to be performed. Default value: Local Legal values: Local, SemiGlobal
+.IP
+Input:
+.TP
+\fB\-i\fR, \fB\-\-inFile\fR [string(s)]
+Input file(s) containing queries in FastA or FastQ format (gzip or zip ok). Mandatory option.
+.TP
+\fB\-d\fR, \fB\-\-index\fR [string]
+Index directory as generated by malt-build. Mandatory option.
+.IP
+Output:
+.TP
+\fB\-o\fR, \fB\-\-output\fR [string(s)]
+Output RMA file(s) or directory or stdout.
+.TP
+\fB\-iu\fR, \fB\-\-includeUnaligned\fR
+Include unaligned queries in RMA output file. Default value: false.
+.TP
+\fB\-a\fR, \fB\-\-alignments\fR [string(s)]
+Output alignment file(s) or directory or stdout.
+.TP
+\fB\-f\fR, \fB\-\-format\fR [string]
+Alignment output format. Default value: SAM Legal values: SAM, Tab, Text
+.TP
+\fB\-za\fR, \fB\-\-gzipAlignments\fR
+Compress alignments using gzip. Default value: true.
+.TP
+\fB\-ssc\fR, \fB\-\-samSoftClip\fR
+Use soft clipping in SAM files (BlastN mode only). Default value: false.
+.TP
+\fB\-sps\fR, \fB\-\-sparseSAM\fR
+Produce sparse SAM format (smaller, faster, but only suitable for MEGAN). Default value: false.
+.TP
+\fB\-oa\fR, \fB\-\-outAligned\fR [string(s)]
+Aligned reads output file(s) or directory or stdout.
+.TP
+\fB\-zal\fR, \fB\-\-gzipAligned\fR
+Compress aligned reads output using gzip. Default value: true.
+.TP
+\fB\-ou\fR, \fB\-\-outUnaligned\fR [string(s)]
+Unaligned reads output file(s) or directory or stdout.
+.TP
+\fB\-zul\fR, \fB\-\-gzipUnaligned\fR
+Compress unaligned reads output using gzip. Default value: true.
+.IP
+Performance:
+.TP
+\fB\-t\fR, \fB\-\-numThreads\fR [number]
+Number of worker threads. Default value: 4.
+.TP
+\fB\-mem\fR, \fB\-\-memoryMode\fR [string]
+Memory mode. Default value: load Legal values: load, page, map
+.TP
+\fB\-mt\fR, \fB\-\-maxTables\fR [number]
+Set the maximum number of seed tables to use (0=all). Default value: 0.
+.TP
+\fB\-rqc\fR, \fB\-\-replicateQueryCache\fR
+Cache results for replicated queries. Default value: false.
+.IP
+Filter:
+.TP
+\fB\-b\fR, \fB\-\-minBitScore\fR [number]
+Minimum bit score. Default value: 50.0.
+.TP
+\fB\-e\fR, \fB\-\-maxExpected\fR [number]
+Maximum expected score. Default value: 1.0.
+.TP
+\fB\-id\fR, \fB\-\-minPercentIdentity\fR [number]
+Minimum percent identity. Default value: 0.0.
+.TP
+\fB\-mq\fR, \fB\-\-maxAlignmentsPerQuery\fR [number]
+Maximum number of alignments per query. Default value: 25.
+.TP
+\fB\-mrf\fR, \fB\-\-maxAlignmentsPerRef\fR [number]
+Maximum number of (non\-overlapping) alignments per reference. Default value: 1.
+.IP
+BlastN parameters:
+.TP
+\fB\-ma\fR, \fB\-\-matchScore\fR [number]
+Match score. Default value: 2.
+.TP
+\fB\-mm\fR, \fB\-\-mismatchScore\fR [number]
+Mismatch score. Default value: \fB\-3\fR.
+.TP
+\fB\-la\fR, \fB\-\-setLambda\fR [number]
+Parameter Lambda for BLASTN statistics. Default value: 0.625.
+.TP
+\fB\-K\fR, \fB\-\-setK\fR [number]
+Parameter K for BLASTN statistics. Default value: 0.41.
+.IP
+BlastP and BlastX parameters:
+.TP
+\fB\-psm\fR, \fB\-\-subMatrix\fR [string]
+Protein substitution matrix to use. Default value: BLOSUM62 Legal values: BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90
+.IP
+DNA query parameters:
+.TP
+\fB\-fo\fR, \fB\-\-forwardOnly\fR
+Align query forward strand only. Default value: false.
+.TP
+\fB\-ro\fR, \fB\-\-reverseOnly\fR
+Align query reverse strand only. Default value: false.
+.IP
+LCA parameters:
+.TP
+\fB\-top\fR, \fB\-\-topPercent\fR [number]
+Top percent value for LCA algorithm. Default value: 10.0.
+.TP
+\fB\-supp\fR, \fB\-\-minSupportPercent\fR [number]
+Min support value for LCA algorithm as a percent of assigned reads (0==off). Default value: 0.001.
+.TP
+\fB\-sup\fR, \fB\-\-minSupport\fR [number]
+Min support value for LCA algorithm (overrides \fB\-\-minSupportPercent\fR). Default value: 0.
+.TP
+\fB\-mpi\fR, \fB\-\-minPercentIdentityLCA\fR [number]
+Min percent identity used by LCA algorithm. Default value: 0.0.
+.TP
+\fB\-mif\fR, \fB\-\-useMinPercentIdentityFilterLCA\fR
+Use percent identity assignment filter. Default value: false.
+.TP
+\fB\-wlca\fR, \fB\-\-weightedLCA\fR
+Use the weighted LCA for taxonomic assignment. Default value: false.
+.TP
+\fB\-lcp\fR, \fB\-\-lcaCoveragePercent\fR [number]
+Set the percent for the LCA to cover. Default value: 100.0.
+.TP
+\fB\-mag\fR, \fB\-\-magnitudes\fR
+Reads have magnitudes (to be used in taxonomic or functional analysis). Default value: false.
+.TP
+\fB\-cf\fR, \fB\-\-conFile\fR [string]
+File of contaminant taxa (one Id or name per line).
+.IP
+Heuristics:
+.TP
+\fB\-spf\fR, \fB\-\-maxSeedsPerFrame\fR [number]
+Maximum number of seed matches per offset per read frame. Default value: 100.
+.TP
+\fB\-spr\fR, \fB\-\-maxSeedsPerRef\fR [number]
+Maximum number of seed matches per read and reference. Default value: 20.
+.TP
+\fB\-sh\fR, \fB\-\-seedShift\fR [number]
+Seed shift. Default value: 1.
+.IP
+Banded alignment parameters:
+.TP
+\fB\-go\fR, \fB\-\-gapOpen\fR [number]
+Gap open penalty. Default value: 11.
+.TP
+\fB\-ge\fR, \fB\-\-gapExtend\fR [number]
+Gap extension penalty. Default value: 1.
+.TP
+\fB\-bd\fR, \fB\-\-band\fR [number]
+Band width/2 for banded alignment. Default value: 4.
+.IP
+Other:
+.TP
+\fB\-rqcb\fR, \fB\-\-replicateQueryCacheBits\fR [number]
+Bits used for caching replicate queries (size is then 2^bits). Default value: 20.
+.TP
+\fB\-xP\fR, \fB\-\-xPart\fR
+Show part of the table in human readable form for debugging. Default value: false.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Echo commandline options and be verbose. Default value: false.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show program usage and quit.
+.SH
+AUTHOR(s)
+.IP
+Daniel H. Huson.
+.PP
+.SH SEE ALSO
+.BR malt-build (1)
View it on GitLab: https://salsa.debian.org/med-team/malt/-/compare/f13eb91498ec7f683b2b34c863567287dc0d172d...ae0376d4b296266235eaa9fc52c197296f6f3f23
--
View it on GitLab: https://salsa.debian.org/med-team/malt/-/compare/f13eb91498ec7f683b2b34c863567287dc0d172d...ae0376d4b296266235eaa9fc52c197296f6f3f23
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