[med-svn] [Git][med-team/flye][master] 2 commits: Add manpage
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 5 18:55:49 BST 2020
Andreas Tille pushed to branch master at Debian Med / flye
Commits:
4d800612 by Andreas Tille at 2020-06-05T18:30:52+02:00
Add manpage
- - - - -
23e7d2f2 by Andreas Tille at 2020-06-05T19:55:24+02:00
Set PATH to minimap2 and samtools
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/flye.1
- + debian/manpages
- debian/patches/use_debian_packaged_libs.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
flye (2.7.1+dfsg-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #962292)
-- Andreas Tille <tille at debian.org> Fri, 05 Jun 2020 15:05:08 +0200
=====================================
debian/control
=====================================
@@ -20,7 +20,9 @@ Package: flye
Architecture: any
Depends: ${shlibs:Depends},
${python3:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ minimap2,
+ samtools
Description: de novo assembler for single molecule sequencing reads using repeat graphs
Flye is a de novo assembler for single molecule sequencing reads, such
as those produced by PacBio and Oxford Nanopore Technologies. It is
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,31 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+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=" --help" \
+ --name="Assembly of long reads with repeat graphs" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+# progname=flye-modules
+# No sensible help output
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/flye.1
=====================================
@@ -0,0 +1,114 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH FLYE "1" "June 2020" "flye 2.7.1" "User Commands"
+.SH NAME
+flye \- Assembly of long reads with repeat graphs
+.SH SYNAPSIS
+.B flye
+(\fB\-\-pacbio\-raw\fR | \fB\-\-pacbio\-corr\fR | \fB\-\-pacbio\-hifi\fR | \fB\-\-nano\-raw\fR |
+\fB\-\-nano\-corr\fR | \fB\-\-subassemblies\fR) file1 [file_2 ...]
+\fB\-\-genome\-size\fR SIZE \fB\-\-out\-dir\fR PATH
+.IP
+[\-\-threads int] [\-\-iterations int] [\-\-min\-overlap int]
+[\-\-meta] [\-\-plasmids] [\-\-trestle] [\-\-polish\-target]
+[\-\-keep\-haplotypes] [\-\-debug] [\-\-version] [\-\-help]
+[\-\-resume] [\-\-resume\-from] [\-\-stop\-after]
+.SH DESCRIPTION
+Input reads can be in FASTA or FASTQ format, uncompressed
+or compressed with gz. Currently, PacBio (raw, corrected, HiFi)
+and ONT reads (raw, corrected) are supported. Expected error rates are
+<30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye
+was primarily developed to run on raw reads. Additionally, the
+\fB\-\-subassemblies\fR option performs a consensus assembly of multiple
+sets of high\-quality contigs. You may specify multiple
+files with reads (separated by spaces). Mixing different read
+types is not yet supported. The \fB\-\-meta\fR option enables the mode
+for metagenome/uneven coverage assembly.
+.PP
+You must provide an estimate of the genome size as input,
+which is used for solid k\-mers selection. Standard size
+modifiers are supported (e.g. 5m or 2.6g). In the case
+of metagenome assembly, the expected total assembly size
+should be provided.
+.PP
+To reduce memory consumption for large genome assemblies,
+you can use a subset of the longest reads for initial disjointig
+assembly by specifying \fB\-\-asm\-coverage\fR option. Typically,
+40x coverage is enough to produce good disjointigs.
+.PP
+You can run Flye polisher as a standalone tool using
+\fB\-\-polish\-target\fR option.
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-pacbio\-raw\fR path [path ...]
+PacBio raw reads
+.TP
+\fB\-\-pacbio\-corr\fR path [path ...]
+PacBio corrected reads
+.TP
+\fB\-\-pacbio\-hifi\fR path [path ...]
+PacBio HiFi reads
+.TP
+\fB\-\-nano\-raw\fR path [path ...]
+ONT raw reads
+.TP
+\fB\-\-nano\-corr\fR path [path ...]
+ONT corrected reads
+.TP
+\fB\-\-subassemblies\fR path [path ...]
+high\-quality contigs input
+.TP
+\fB\-g\fR size, \fB\-\-genome\-size\fR size
+estimated genome size (for example, 5m or 2.6g)
+.TP
+\fB\-o\fR path, \fB\-\-out\-dir\fR path
+Output directory
+.TP
+\fB\-t\fR int, \fB\-\-threads\fR int
+number of parallel threads [1]
+.TP
+\fB\-i\fR int, \fB\-\-iterations\fR int
+number of polishing iterations [1]
+.TP
+\fB\-m\fR int, \fB\-\-min\-overlap\fR int
+minimum overlap between reads [auto]
+.TP
+\fB\-\-asm\-coverage\fR int
+reduced coverage for initial disjointig assembly [not
+set]
+.TP
+\fB\-\-plasmids\fR
+rescue short unassembled plasmids
+.TP
+\fB\-\-meta\fR
+metagenome / uneven coverage mode
+.TP
+\fB\-\-keep\-haplotypes\fR
+do not collapse alternative haplotypes
+.TP
+\fB\-\-trestle\fR
+enable Trestle [disabled]
+.TP
+\fB\-\-polish\-target\fR path
+run polisher on the target sequence
+.TP
+\fB\-\-resume\fR
+resume from the last completed stage
+.TP
+\fB\-\-resume\-from\fR stage_name
+resume from a custom stage
+.TP
+\fB\-\-stop\-after\fR stage_name
+stop after the specified stage completed
+.TP
+\fB\-\-debug\fR
+enable debug output
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.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/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -49,3 +49,16 @@ Description: use Debian packaged libminimap2 and liblemon
for file in bin_files:
if not os.path.isfile(os.path.join(build_dir, file)):
sys.exit('Error: binary not found: ' + file)
+--- a/flye/polishing/alignment.py
++++ b/flye/polishing/alignment.py
+@@ -22,8 +22,8 @@ from flye.six.moves import range
+
+
+ logger = logging.getLogger()
+-MINIMAP_BIN = "flye-minimap2"
+-SAMTOOLS_BIN = "flye-samtools"
++MINIMAP_BIN = "/usr/bin/minimap2"
++SAMTOOLS_BIN = "/usr/bin/samtools"
+
+ ContigInfo = namedtuple("ContigInfo", ["id", "length", "type"])
+
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/c221816bf964bd6eaca1d38d128328502a1ec2e7...23e7d2f2e78e41a0d98412c97beff94d97723540
--
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/c221816bf964bd6eaca1d38d128328502a1ec2e7...23e7d2f2e78e41a0d98412c97beff94d97723540
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