[med-svn] [Git][med-team/xpore][master] 4 commits: Add pyensmbl to Depends

Fri May 21 19:03:14 BST 2021


Nilesh Patra pushed to branch master at Debian Med / xpore


Commits:
8259f050 by Nilesh Patra at 2021-05-21T23:04:18+05:30
Add pyensmbl to Depends

- - - - -
3e7bc643 by Nilesh Patra at 2021-05-21T17:37:17+00:00
Add manpages

- - - - -
c2fb3162 by Nilesh Patra at 2021-05-21T18:00:24+00:00
Minor change

- - - - -
9ec450c0 by Nilesh Patra at 2021-05-21T18:00:30+00:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/xpore-dataprep.1
- + debian/xpore-diffmod.1
- + debian/xpore.manpages


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-xpore (1.0-1) UNRELEASED; urgency=medium
+xpore (1.0-1) unstable; urgency=medium
 
+  [ Steffen Moeller, Nilesh Patra ]
   * Initial release (Closes:#988690)
 
- -- Steffen Moeller <moeller at debian.org>  Mon, 17 May 2021 18:57:10 +0200
+ -- Steffen Moeller <moeller at debian.org>  Fri, 21 May 2021 23:27:59 +0530


=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Rules-Requires-Root: no
 
 Package: xpore
 Architecture: all
-Depends: ${python3:Depends}, ${misc:Depends}
+Depends: ${python3:Depends}, ${misc:Depends}, pyensembl
 Suggests: xpore-doc
 Description: Nanopore analysis of differential RNA modifications
  RNA is transcribed from DNA, possibly spliced and exported to the


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,35 @@
+#!/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 $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=xpore-dataprep
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=xpore-diffmod
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/xpore.manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+


=====================================
debian/xpore-dataprep.1
=====================================
@@ -0,0 +1,84 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH XPORE-DATAPREP "1" "May 2021" "xpore-dataprep 1.0" "User Commands"
+.SH NAME
+xpore-dataprep \- Nanopore analysis of differential RNA modifications
+.SH DESCRIPTION
+usage: xpore\-dataprep [\-h] \fB\-\-eventalign\fR EVENTALIGN \fB\-\-summary\fR SUMMARY \fB\-\-out_dir\fR
+.TP
+OUT_DIR [\-\-ensembl ENSEMBL] [\-\-species SPECIES]
+[\-\-customised_genome] [\-\-reference_name REFERENCE_NAME]
+[\-\-annotation_name ANNOTATION_NAME]
+[\-\-gtf_path_or_url GTF_PATH_OR_URL]
+[\-\-transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS]
+[\-\-skip_eventalign_indexing] [\-\-genome]
+[\-\-n_processes N_PROCESSES] [\-\-chunk_size CHUNK_SIZE]
+[\-\-readcount_min READCOUNT_MIN]
+[\-\-readcount_max READCOUNT_MAX] [\-\-resume]
+.SS "required arguments:"
+.TP
+\fB\-\-eventalign\fR EVENTALIGN
+eventalign filepath, the output from nanopolish.
+(default: None)
+.TP
+\fB\-\-summary\fR SUMMARY
+eventalign summary filepath, the output from
+nanopolish. (default: None)
+.TP
+\fB\-\-out_dir\fR OUT_DIR
+output directory. (default: None)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-ensembl\fR ENSEMBL
+ensembl version for gene\-transcript mapping. (default:
+91)
+.TP
+\fB\-\-species\fR SPECIES
+species for ensembl gene\-transcript mapping. (default:
+homo_sapiens)
+.TP
+\fB\-\-customised_genome\fR
+if customised genome provided. (default: False)
+.TP
+\fB\-\-reference_name\fR REFERENCE_NAME
+fasta reference name. (default: None)
+.TP
+\fB\-\-annotation_name\fR ANNOTATION_NAME
+gtf annotation name. (default: None)
+.TP
+\fB\-\-gtf_path_or_url\fR GTF_PATH_OR_URL
+gtf file path or url. (default: None)
+.TP
+\fB\-\-transcript_fasta_paths_or_urls\fR TRANSCRIPT_FASTA_PATHS_OR_URLS
+transcript fasta paths or urls. (default: None)
+.TP
+\fB\-\-skip_eventalign_indexing\fR
+skip indexing the eventalign nanopolish output.
+(default: False)
+.TP
+\fB\-\-genome\fR
+to run on Genomic coordinates. Without this argument,
+the program will run on transcriptomic coordinates
+(default: False)
+.TP
+\fB\-\-n_processes\fR N_PROCESSES
+number of processes to run. (default: 1)
+.TP
+\fB\-\-chunk_size\fR CHUNK_SIZE
+number of lines from nanopolish eventalign.txt for
+processing. (default: 1000000)
+.TP
+\fB\-\-readcount_min\fR READCOUNT_MIN
+minimum read counts per gene. (default: 1)
+.TP
+\fB\-\-readcount_max\fR READCOUNT_MAX
+maximum read counts per gene. (default: 1000)
+.TP
+\fB\-\-resume\fR
+with this argument, the program will resume from the
+previous run. (default: False)
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/xpore-diffmod.1
=====================================
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH XPORE-DIFFMOD "1" "May 2021" "xpore-diffmod 1.0" "User Commands"
+.SH NAME
+xpore-diffmod \- Nanopore analysis of differential RNA modifications
+.SH DESCRIPTION
+usage: xpore\-diffmod [\-h] \fB\-\-config\fR CONFIG [\-\-n_processes N_PROCESSES]
+.IP
+[\-\-save_models] [\-\-resume] [\-\-ids [IDS ...]]
+.SS "required arguments:"
+.TP
+\fB\-\-config\fR CONFIG
+yaml configuraion filepath. (default: None)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-n_processes\fR N_PROCESSES
+number of processes to run. (default: 1)
+.TP
+\fB\-\-save_models\fR
+with this argument, the program will save the model
+parameters for each id. (default: False)
+.TP
+\fB\-\-resume\fR
+with this argument, the program will resume from the
+previous run. (default: False)
+.TP
+\fB\-\-ids\fR [IDS ...]
+gene / transcript ids to model. (default: [])
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/xpore.manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1



View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f

-- 
View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f
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