[med-svn] [Git][med-team/clonalframeml][master] 2 commits: Added test for the package analysis

[Israel Komolehin (@Komolehin)]

Israel Komolehin pushed to branch master at Debian Med / clonalframeml


Commits:
c89d193c by Komolehin Israel Timilehin at 2024-01-24T09:40:40+00:00
Added test for the package analysis

- - - - -
bac98550 by Komolehin Israel Timilehin at 2024-01-24T09:41:35+00:00
Added README to document how to run the test and test observation

- - - - -


2 changed files:

- + debian/tests/README.md
- + debian/tests/run-unit-test


Changes:

=====================================
debian/tests/README.md
=====================================
@@ -0,0 +1,8 @@
+## Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+#### Note! This is a real-world example, and requires around 12 hours of run time.
+
+`sh run-unit-test`
\ No newline at end of file


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,23 @@
+#!/bin/bash -e
+
+pkg=clonalframeml
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+
+	AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`
+	trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+cd "$AUTOPKGTEST_TMP"/
+
+# Download data
+wget -O clmf.tgz https://figshare.com/ndownloader/files/34861005
+
+# Unzip data
+tar -xzvf clmf.tgz
+
+cd ClonalFrameML
+
+# Run the standard ClonalFrameML analysis as follows. Note! This is a real-world example, and requires around 12 hours of run time.
+ClonalFrameML Saureus.phyML.newick Saureus.fasta example.output -kappa 4.967695 -emsim 100 -ignore_user_sites Saureus.non-core-sites.txt > example.log
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/clonalframeml/-/compare/0e8c95683dc9cb0b3a778bc588084cd087f8f284...bac98550596e087efba2ec01ec024e83eee2c4c7

-- 
View it on GitLab: https://salsa.debian.org/med-team/clonalframeml/-/compare/0e8c95683dc9cb0b3a778bc588084cd087f8f284...bac98550596e087efba2ec01ec024e83eee2c4c7
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