Steffen Möller pushed to branch master at Debian Med / npinv
Commits:
1b38eb4a by Steffen at 2021-07-11T21:30:38+02:00
Towards lintian-cleanliness.
- - - - -
8 changed files:
- debian/control
- + debian/manpages
- + debian/npInv
- + debian/npInv.1
- + debian/npinv.dirs
- + debian/npinv.install
- + debian/npinv.links
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -16,7 +16,11 @@ Rules-Requires-Root: no
Package: npinv
Architecture: all
-Depends: ${misc:Depends}
+Depends: ${misc:Depends},
+ libcommons-math3-java,
+ libpicard-java,
+ libhtsjdk-java,
+ jarwrapper
Description: finds inversions in long DNA segments post alignment
npInv accurately detects and genotypes inversions using multiple
alignment long reads.
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/npInv.1
=====================================
debian/npInv
=====================================
@@ -0,0 +1,2 @@
+#!/bin/sh
+java -cp
/usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar
-jar /usr/share/java/npInv.jar $*
=====================================
debian/npInv.1
=====================================
@@ -0,0 +1,21 @@
+.TH NPINV "1" "July 2021" "npInv 1.24" "User Commands"
+.SH NAME
+npInv \- npInv
+.SH DESCRIPTION
+Program function: Read a SE bam file and get the inversion
+Version: 1.24
+\fB\-\-output[String]\fR file to write
+\fB\-\-input[String]\fR file to read
+optional:
+\fB\-\-region[String]\fR Specify the region for running.
+.IP
+Such as chr9:1\-1000 OR chr9 OR all Default[all]
+.PP
+\fB\-\-minAln[int]\fR minimum size for Alignment & Inv. Default[500]
+\fB\-\-IRdatabase[String]\fR An inverted repeat file for the reference in bed
format. Default[none]
+\fB\-\-min[int]\fR minimum size of an inversion. Default[500]
+\fB\-\-max[int]\fR maximum size of an inversion. Default[10000]
+\fB\-\-window[int]\fR minimun window size (bp) to merge inversion breakpoints.
Default[2000]
+\fB\-\-threshold[int]\fR minimum number of supporting reads for an inversion.
Default[3]
+\fB\-\-help\fR Show usage
+For example: java \fB\-jar\fR npInv.jar \fB\-\-input\fR sample.bam
\fB\-\-output\fR sample.VCF
=====================================
debian/npinv.dirs
=====================================
@@ -0,0 +1 @@
+usr/share/java
=====================================
debian/npinv.install
=====================================
@@ -0,0 +1,2 @@
+npInv*.jar usr/share/java/
+debian/npInv usr/bin/
=====================================
debian/npinv.links
=====================================
@@ -0,0 +1 @@
+usr/share/java/npInv-1.24.jar usr/share/java/npInv.jar
=====================================
debian/rules
=====================================
@@ -4,18 +4,19 @@
dh $@
CLASSPATH=/usr/share/java/htsjdk.jar:/usr/share/java/picard.jar:/usr/share/java/commons-math3.jar
+VERSION=1.24
override_dh_auto_build:
ln -s . inversion
javac -cp $(CLASSPATH) inversion/*.java
mkdir -p META-INF
cp debian/MANIFEST.MF META-INF
- jar cmvf META-INF/MANIFEST.MF npInv.jar inversion/*.class
inversion/*.java
- chmod +x npInv.jar
+ jar cmvf META-INF/MANIFEST.MF npInv-$(VERSION).jar inversion/*.class
#inversion/*.java
+ chmod +x npInv-$(VERSION).jar
rm -rf META-INF inversion
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- java -cp
/usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar
-jar npInv.jar --help
+ java -cp
/usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar
-jar npInv-$(VERSION).jar --help
endif
override_dh_auto_clean:
View it on GitLab:
https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1
--
View it on GitLab:
https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1
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