[med-svn] [Git][med-team/megahit][master] Autopkgtest

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / megahit


Commits:
39fac626 by Shayan Doust at 2019-10-17T21:36:50Z
Autopkgtest
Temp remove the patch for the source fix (pbuilder failed) as this is problematic

- - - - -


2 changed files:

- debian/patches/series
- debian/tests/run-unit-test


Changes:

=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
 fix_test_path.patch
 2to3.patch
-fix_src_packed_field.patch


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,19 +1,26 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=megahit
 
 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}"
+cp -a /usr/share/doc/${pkg}/data/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
+gunzip r3_1.fa.gz r3_2.fa.gz
+
+megahit --test -t 2
+MEGAHIT_NUM_MERCY_FACTOR=1.5 megahit --test -t 4 --mem-flag 0 --no-hw-accel
+megahit --test -t 2 --kmin-1pass
+rm -rf test-random && python3 generate_random_fasta.py > random.fa && megahit -r random.fa --k-list 255 --min-count 1 -o test-random
+rm -rf test-fastg && megahit --test -t 2 --mem-flag 2 --keep-tmp-files -o test-fastg
+megahit_toolkit contig2fastg 59 test-fastg/intermediate_contigs/k59.contigs.fa > 59.fastg
+megahit_toolkit readstat < test-fastg/intermediate_contigs/k59.contigs.fa
+
 
-#do_stuff_to_test_package#



View it on GitLab: https://salsa.debian.org/med-team/megahit/commit/39fac62663cad276a5e17cee1f34e7f06baee4d9

-- 
View it on GitLab: https://salsa.debian.org/med-team/megahit/commit/39fac62663cad276a5e17cee1f34e7f06baee4d9
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