[med-svn] [Git][med-team/idba][master] 4 commits: Sorry for giving incomplete advise
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 10 14:51:53 GMT 2020
Andreas Tille pushed to branch master at Debian Med / idba
Commits:
b6b63558 by Andreas Tille at 2020-03-10T15:22:12+01:00
Sorry for giving incomplete advise
- - - - -
37f99865 by Andreas Tille at 2020-03-10T15:47:21+01:00
Add few manpages for tools inside idba-extra (more would be nice)
- - - - -
69e7cf44 by Andreas Tille at 2020-03-10T15:49:12+01:00
sim_reads.1
- - - - -
e3674ada by Andreas Tille at 2020-03-10T15:51:23+01:00
sim_reads_tran.1
- - - - -
14 changed files:
- debian/changelog
- debian/control
- debian/createmanpages
- + debian/idba-extra.manpages
- + debian/idba-extra/filter_blat.1
- + debian/idba-extra/filter_contigs.1
- + debian/idba-extra/fq2fa.1
- + debian/idba-extra/sim_reads.1
- + debian/idba-extra/sim_reads_tran.1
- debian/idba.manpages
- debian/idba.1 → debian/idba/idba.1
- debian/idba_hybrid.1 → debian/idba/idba_hybrid.1
- debian/idba_tran.1 → debian/idba/idba_tran.1
- debian/idba_ud.1 → debian/idba/idba_ud.1
Changes:
=====================================
debian/changelog
=====================================
@@ -7,18 +7,17 @@ idba (1.1.3-6) UNRELEASED; urgency=medium
* Generate testing data and add test_data/README
* Add autopkgtests in run-unit-test (Closes: #909716)
* Added debian/README.test
+ * Switched to debian/examples from debian/install
+ * Added another binary, idba-extra
+ * Removed files that can be generated during testing
+ * Modified autopkgtests to generate data
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Set upstream metadata fields: Bug-Database, Repository.
* Make sure sim_reads will be found in test suite
-
- [ Pranav Ballaney ]
- * Switched to debian/examples from debian/install
- * Added another binary, idba-extra
- * Removed files that can be generated during testing
- * Modified autopkgtests to generate data
+ * Add few manpages for tools inside idba-extra (more would be nice)
-- Pranav Ballaney <ballaneypranav at gmail.com> Tue, 10 Mar 2020 01:12:44 +0530
=====================================
debian/control
=====================================
@@ -43,5 +43,21 @@ Depends: ${shlibs:Depends},
idba
Description: iterative De Bruijn Graph short read assemblers (extra tools)
IDBA stands for iterative de Bruijn graph assembler. In computational
- ...
- This package ships extra tools for using idba in specific situations.
\ No newline at end of file
+ sequence biology, an assembler solves the puzzle coming from large
+ sequencing machines that feature many gigabytes of short reads from a
+ large genome.
+ .
+ This package provides several flavours of the IDBA assembler, as they all
+ share the same source tree but serve different purposes and evolved over time.
+ .
+ IDBA is the basic iterative de Bruijn graph assembler for
+ second-generation sequencing reads. IDBA-UD, an extension of IDBA,
+ is designed to utilize paired-end reads to assemble low-depth regions
+ and use progressive depth on contigs to reduce errors in high-depth
+ regions. It is a generic purpose assembler and especially good for
+ single-cell and metagenomic sequencing data. IDBA-Hybrid is another
+ update version of IDBA-UD, which can make use of a similar reference
+ genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
+ graph assembler for RNA-Seq data.
+ .
+ This package ships extra tools for using idba in specific situations.
=====================================
debian/createmanpages
=====================================
@@ -1,10 +1,84 @@
#!/bin/sh
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
-MANDIR=debian
+MANDIR=debian/idba
mkdir -p $MANDIR
-for i in idba idba_tran idba_hybrid idba_ud
-do
- help2man --no-info --no-discard-stderr \
- --name='Iterative de Bruijn Graph Assembler for hybrid sequencing data' \
- --version-string="$VERSION" bin/$i | grep -v "unknown option" | grep -v "bin/idba" > $MANDIR/$i.1
-done
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Iterative de Bruijn Graph Assembler" \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=idba_tran
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Iterative de Bruijn Graph Assembler for next-generation transcriptome sequencing data." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=idba_hybrid
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Iterative de Bruijn Graph Assembler for hybrid sequencing data." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=idba_ud
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/${PROGNAME}.manpages
+
+################ for idba-extra package
+
+MANDIR=debian/idba-extra
+mkdir -p $MANDIR
+
+progname=fq2fa
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Convert Fastq sequences to Fasta sequences." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=filter_blat
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Validate contigs by blat." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=filter_contigs
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Simulate sequencing reads from references." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sim_reads
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Convert Fastq sequences to Fasta sequences." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sim_reads_tran
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="Simulate sequencing reads from transcripts references and expression level profile." \
+ --version-string="$VERSION" ${progname} | grep -v -e "unknown option" -e "not enough parameters" > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+
+echo "$MANDIR/*.1" > debian/idba-extra.manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/idba-extra.manpages
=====================================
@@ -0,0 +1 @@
+debian/idba-extra/*.1
=====================================
debian/idba-extra/filter_blat.1
=====================================
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH FILTER_BLAT "1" "March 2020" "filter_blat 1.1.3" "User Commands"
+.SH NAME
+filter_blat \- Validate contigs by blat.
+.SH SYNOPSIS
+.B validate_contigs_blat
+\fI\,ref.fa contigs.fa.\/\fR
+.SH DESCRIPTION
+filter_blat: invalid option \fB\-\-\fR 'h'
+validate_contigs_blat \- validate contigs by blat.
+.SS "Allowed Options:"
+.TP
+\fB\-\-min_contig\fR arg (=100)
+minimum contigs
+.TP
+\fB\-\-similar\fR arg (=0.95)
+similarity
+.TP
+\fB\-\-is_local\fR
+is local
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba-extra/filter_contigs.1
=====================================
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH FILTER_CONTIGS "1" "March 2020" "filter_contigs 1.1.3" "User Commands"
+.SH NAME
+filter_contigs \- Simulate sequencing reads from references.
+.SH SYNOPSIS
+.B fq2fa
+\fI\,tmp.fq tmp.fa \/\fR[...]
+.SH DESCRIPTION
+filter_contigs \- Convert Fastq sequences to Fasta sequences.
+.IP
+fq2fa \fB\-\-paired\fR tmp.fq tmp.fa
+fq2fa \fB\-\-merge\fR tmp_1.fq tmp_2.fq tmp.fa
+.SS "Allowed Options:"
+.TP
+\fB\-\-min_contig\fR arg (=100)
+filter out reads containing 'N'
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba-extra/fq2fa.1
=====================================
@@ -0,0 +1,25 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH FQ2FA "1" "March 2020" "fq2fa 1.1.3" "User Commands"
+.SH NAME
+fq2fa \- Convert Fastq sequences to Fasta sequences.
+.SH SYNOPSIS
+.B fq2fa
+\fI\,tmp.fq tmp.fa \/\fR[...]
+.SH DESCRIPTION
+fq2fa \- Convert Fastq sequences to Fasta sequences.
+.IP
+fq2fa \fB\-\-paired\fR tmp.fq tmp.fa
+fq2fa \fB\-\-merge\fR tmp_1.fq tmp_2.fq tmp.fa
+.SS "Allowed Options:"
+.TP
+\fB\-\-paired\fR
+if the reads are paired\-end in one file
+.TP
+\fB\-\-merge\fR
+if the reads are paired\-end in two files
+.TP
+\fB\-\-filter\fR
+filter out reads containing 'N'
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba-extra/sim_reads.1
=====================================
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH SIM_READS "1" "March 2020" "sim_reads 1.1.3" "User Commands"
+.SH NAME
+sim_reads \- Convert Fastq sequences to Fasta sequences.
+.SH SYNOPSIS
+.B sim_reads
+\fI\,ref.fa reads.fa\/\fR
+.SH DESCRIPTION
+sim_reads \- Simulate sequencing reads from references.
+.SS "Allowed Options:"
+.TP
+\fB\-\-depth\fR arg (=30)
+sequencing depth of the sample
+.TP
+\fB\-\-error_rate\fR arg (=0.01)
+error rate
+.TP
+\fB\-\-read_length\fR arg (=100)
+read length
+.TP
+\fB\-\-paired\fR
+if paired\-end
+.TP
+\fB\-\-sd\fR arg (=\-1)
+sd
+.TP
+\fB\-\-insert_distance\fR arg (=500)
+insert distance
+.TP
+\fB\-\-print_correct\fR
+output correct reads
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba-extra/sim_reads_tran.1
=====================================
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH SIM_READS_TRAN "1" "March 2020" "sim_reads_tran 1.1.3" "User Commands"
+.SH NAME
+sim_reads_tran \- Simulate sequencing reads from transcripts references and expression level profile.
+.SH SYNOPSIS
+.B sim_reads_tran
+\fI\,ref.fa reads.fa\/\fR
+.SH DESCRIPTION
+sim_reads_tran \- Simulate sequencing reads from transcripts references and expression level profile.
+.SS "Allowed Options:"
+.TP
+\fB\-\-error_rate\fR arg (=0.01)
+error rate
+.TP
+\fB\-\-read_length\fR arg (=100)
+read length
+.TP
+\fB\-\-paired\fR
+if paired\-end
+.TP
+\fB\-\-sd\fR arg (=\-1)
+sd
+.TP
+\fB\-\-insert_distance\fR arg (=500)
+insert distance
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba.manpages
=====================================
@@ -1,4 +1 @@
-debian/idba.1
-debian/idba_hybrid.1
-debian/idba_tran.1
-debian/idba_ud.1
+debian/idba/*.1
=====================================
debian/idba.1 → debian/idba/idba.1
=====================================
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH IDBA "1" "August 2017" "idba 1.1.3" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH IDBA "1" "March 2020" "idba 1.1.3" "User Commands"
.SH NAME
-idba \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba \- Iterative de Bruijn Graph Assembler
.SH SYNOPSIS
.B idba_ud
\fI\,-r read.fa -o output_dir\/\fR
@@ -74,3 +74,6 @@ do not do correction
.TP
\fB\-\-pre_correction\fR
perform pre\-correction before assembly
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba_hybrid.1 → debian/idba/idba_hybrid.1
=====================================
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH IDBA_HYBRID "1" "August 2017" "idba_hybrid 1.1.3" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH IDBA_HYBRID "1" "March 2020" "idba_hybrid 1.1.3" "User Commands"
.SH NAME
-idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data.
.SH SYNOPSIS
.B idba_hybrid
\fI\,-r read.fa -o output_dir \/\fR[\fI\,--reference ref.fa\/\fR]
@@ -92,3 +92,6 @@ do not do correction
.TP
\fB\-\-pre_correction\fR
perform pre\-correction before assembly
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba_tran.1 → debian/idba/idba_tran.1
=====================================
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH IDBA_TRAN "1" "August 2017" "idba_tran 1.1.3" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH IDBA_TRAN "1" "March 2020" "idba_tran 1.1.3" "User Commands"
.SH NAME
-idba_tran \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba_tran \- Iterative de Bruijn Graph Assembler for next-generation transcriptome sequencing data.
.SH SYNOPSIS
.B idba_tran
\fI\,-r read.fa -o output_dir\/\fR
@@ -77,3 +77,6 @@ maximum number of isoforms
.TP
\fB\-\-max_component_size\fR arg (=30)
maximum size of components
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/idba_ud.1 → debian/idba/idba_ud.1
=====================================
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH IDBA_UD "1" "August 2017" "idba_ud 1.1.3" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH IDBA_UD "1" "March 2020" "idba_ud 1.1.3" "User Commands"
.SH NAME
-idba_ud \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba_ud \- Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.
.SH SYNOPSIS
.B idba_ud
\fI\,-r read.fa -o output_dir\/\fR
@@ -86,3 +86,6 @@ do not do correction
.TP
\fB\-\-pre_correction\fR
perform pre\-correction before assembly
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/idba/-/compare/04c4e1ba726710c2da2574a2747ca4acb6097464...e3674adaf4a0140a71427265335f9b968da73f14
--
View it on GitLab: https://salsa.debian.org/med-team/idba/-/compare/04c4e1ba726710c2da2574a2747ca4acb6097464...e3674adaf4a0140a71427265335f9b968da73f14
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