[med-svn] [Git][med-team/lumpy-sv][master] 3 commits: Bamkit is about to be uploaded to new

[Andreas Tille]

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


Commits:
eaa7dcc3 by Andreas Tille at 2020-06-01T22:19:24+02:00
Bamkit is about to be uploaded to new

- - - - -
dee6e8cf by Andreas Tille at 2020-06-01T23:05:16+02:00
Remove autopkgtest template

- - - - -
e64a6554 by Andreas Tille at 2020-06-01T23:20:10+02:00
Adapt check to Python3

- - - - -


8 changed files:

- − debian/README.test
- debian/changelog
- debian/control
- debian/etc/lumpyexpress.config
- debian/install
- debian/patches/lumpyexpress.config.patch
- − debian/tests/control
- − debian/tests/run-unit-test


Changes:

=====================================
debian/README.test deleted
=====================================
@@ -1,8 +0,0 @@
-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/changelog
=====================================
@@ -1,6 +1,5 @@
-lumpy-sv (0.3.0+dfsg-2) UNRELEASED; urgency=medium
+lumpy-sv (0.3.0+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #961998)
-  TODO: https://salsa.debian.org/med-team/bamkit
 
  -- Andreas Tille <tille at debian.org>  Mon, 01 Jun 2020 21:58:38 +0200


=====================================
debian/control
=====================================
@@ -27,7 +27,8 @@ Depends: ${shlibs:Depends},
          samtools,
          python3,
          python3-pysam,
-         python3-numpy
+         python3-numpy,
+         bamkit
 Recommends: sambamba
 Description: general probabilistic framework for structural variant discovery
  LUMPY, a novel SV discovery framework that naturally integrates multiple


=====================================
debian/etc/lumpyexpress.config
=====================================
@@ -8,6 +8,6 @@ SAMTOOLS=/usr/bin/samtools
 PYTHON=/usr/bin/python3
 
 PAIREND_DISTRO=/usr/share/lumpy-sv/scripts/pairend_distro.py
-#BAMGROUPREADS=/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
-#BAMFILTERRG=/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
-#BAMLIBS=/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
+BAMGROUPREADS=/usr/share/bamkit/bamgroupreads.py
+BAMFILTERRG=/usr/share/bamkit/bamfilterrg.py
+BAMLIBS=/usr/share/bamkit/bamlibs.py


=====================================
debian/install
=====================================
@@ -1,4 +1,4 @@
-debian/etc/lumpyexpress.config	etc/lumpy
+debian/etc/lumpyexpress.config	etc/lumpy-sv
 scripts				usr/share/lumpy-sv
 bin/lumpy			usr/bin
 bin/lumpy_filter		usr/bin


=====================================
debian/patches/lumpyexpress.config.patch
=====================================
@@ -21,6 +21,17 @@ Description: Adapt paths to Debian locations
  
      # For testing if the full BAM is actually a CRAM!
      HEXDUMP=`which hexdump || true`
+@@ -92,8 +92,8 @@ check_python_modules() {
+     PYTHON_TEST=$1
+     echo -e "\nChecking for required python modules ($PYTHON_TEST)..."
+ 
+-    $PYTHON_TEST -c "import imp; imp.find_module('pysam')"
+-    $PYTHON_TEST -c "import imp; imp.find_module('numpy')"
++    $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')"
++    $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')"
+ }
+ 
+ ## usage
 @@ -126,7 +126,7 @@ options:
  
  # set defaults


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


=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
-  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
-  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#



View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c

-- 
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c
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