[med-svn] [Git][med-team/lumpy-sv][master] 2 commits: Remove additional hash sign

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / lumpy-sv


Commits:
2a32d78a by Andreas Tille at 2020-06-02T21:36:56+02:00
Remove additional hash sign

- - - - -
3a44f943 by Andreas Tille at 2020-06-02T21:47:04+02:00
Start working on tests

- - - - -


9 changed files:

- + debian/README.test
- debian/control
- + debian/lumpy-sv-examples.install
- + debian/lumpy-sv.docs
- debian/install → debian/lumpy-sv.install
- + debian/patches/fix_shebang.patch
- debian/patches/series
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/control
=====================================
@@ -35,3 +35,15 @@ Description: general probabilistic framework for structural variant discovery
  SV signals jointly across multiple samples.  LUMPY yields improved
  sensitivity, especially when SV signal is reduced owing to either low
  coverage data or low intra-sample variant allele frequency.
+
+Package: lumpy-sv-examples
+Architecture: all
+Depends: ${misc:Depends},
+Enhances: lumpy-sv
+Description: general probabilistic framework for structural variant discovery (data)
+ LUMPY, a novel SV discovery framework that naturally integrates multiple
+ SV signals jointly across multiple samples.  LUMPY yields improved
+ sensitivity, especially when SV signal is reduced owing to either low
+ coverage data or low intra-sample variant allele frequency.
+ .
+ This package contains some example data and scripts to test lumpy-sv.


=====================================
debian/lumpy-sv-examples.install
=====================================
@@ -0,0 +1,3 @@
+data		usr/share/doc/lumpy-sv/examples
+lumpy_tests	usr/share/doc/lumpy-sv/examples
+test		usr/share/doc/lumpy-sv/examples


=====================================
debian/lumpy-sv.docs
=====================================
@@ -0,0 +1 @@
+README*


=====================================
debian/install → debian/lumpy-sv.install
=====================================


=====================================
debian/patches/fix_shebang.patch
=====================================
@@ -0,0 +1,36 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 26 May 2020 15:07:58 +0200
+Description: Remove additional hash sign
+
+--- a/test/bp_pe.sh
++++ b/test/bp_pe.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+ 
+ if [ -z $5 ]
+ then
+--- a/test/bp_pe_pl.sh
++++ b/test/bp_pe_pl.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+ 
+ if [ -z $5 ]
+ then
+--- a/test/bp_pesr.sh
++++ b/test/bp_pesr.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+ 
+ if [ -z $7 ]
+ then
+--- a/test/bp_pesr_pl.sh
++++ b/test/bp_pesr_pl.sh
+@@ -1,4 +1,4 @@
+-##!/bin/bash
++#!/bin/bash
+ 
+ if [ -z $7 ]
+ then


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 use_debian_packaged_libs.patch
 lumpyexpress.config.patch
+fix_shebang.patch


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,30 @@
+#!/bin/bash
+set -e
+
+pkg=lumpy-sv
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+#  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+set -x
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+cd test
+
+sed -i -e 's:\.\./scripts:/usr/share/lumpy-sv/scripts:' \
+       -e 's:\.\./bin/lumpy:/usr/bin/lumpy:' \
+    *.sh 
+
+./test.sh
+
+# Testing lumpy paired-end
+# ./bp_pe_pl.sh: line 26 refers to /usr/share/lumpy-sv/scripts/pairend_distro.pl
+# but there is only /usr/share/lumpy-sv/scripts/pairend_distro.py ... but with different options
+./test_pl.sh
+#  --> contact upstream
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/e64a65545fbf60c5c98965bc1d00d416b2f9582c...3a44f943ef37ae1ee666ff7a9e966adfd2c0e5c5

-- 
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/e64a65545fbf60c5c98965bc1d00d416b2f9582c...3a44f943ef37ae1ee666ff7a9e966adfd2c0e5c5
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