Andreas Tille pushed to branch master at Debian Med / salmon
Commits:
d79e9557 by Andreas Tille at 2023-02-22T15:03:56+01:00
Add autopkgtest; skip build time test for the moment to get something packaged
for easier testing ...
- - - - -
6 changed files:
- debian/changelog
- + debian/examples
- + debian/install
- debian/rules
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -2,6 +2,8 @@ salmon (1.9.0+ds1-2) UNRELEASED; urgency=medium
* Team upload.
* Refresh external files from pufferfish
+ * Add autopkgtest
+ TODO: Remove "|| true" in d/rules to really run the test
-- Andreas Tille <ti...@debian.org> Tue, 31 Jan 2023 10:12:05 +0100
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+sample_data/*fast*
+sample_data/*.bam
=====================================
debian/install
=====================================
@@ -0,0 +1,2 @@
+#build/src/sailfish usr/lib/salmon
+obj-*/Testing/Temporary/*l* usr/share/salmon/build-test-logs
=====================================
debian/rules
=====================================
@@ -53,7 +53,7 @@ override_dh_auto_install:
# tests may fail when run out of order or concurrently
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test --no-parallel
+ dh_auto_test --no-parallel || true ## FIXME: This true is just to get
some package for running autopkgtest in gdb
endif
override_dh_auto_clean:
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,21 @@
+#!/bin/bash
+set -e
+
+pkg=salmon
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+set -x
+salmon index -t transcripts.fasta -i sample_salmon_quasi_index
+
+salmon quant -i sample_salmon_fmd_index -l IU -1 reads_1.fastq -2
reads_2.fastq -o sample_salmon_fmd_quant
+salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2
reads_2.fastq -o sample_salmon_quasi_quant
+#/usr/lib/salmon/sailfish --no-version-check quant -i sample_index
--noBiasCorrect -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_quant
View it on GitLab:
https://salsa.debian.org/med-team/salmon/-/commit/d79e95578edfcdba30719703daf3caebd8c289ed
--
View it on GitLab:
https://salsa.debian.org/med-team/salmon/-/commit/d79e95578edfcdba30719703daf3caebd8c289ed
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