[med-svn] [Git][med-team/tigr-glimmer][master] Add autopkgtests

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / tigr-glimmer


Commits:
12b2e3fa by Nilesh Patra at 2020-04-29T20:55:09+05:30
Add autopkgtests

- - - - -


2 changed files:

- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/tests/control
=====================================
@@ -1,3 +1,4 @@
 Tests: run-unit-test
 Depends: @
 Restrictions: allow-stderr
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,48 +1,22 @@
 #!/bin/bash
 set -e
 
-pkg="tigr-glimmer"
+pkg=tigr-glimmer
 
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
 
-cd $AUTOPKGTEST_TMP
-find . -name "*.gz" -exec gunzip \{\} \;
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
 
-echo "g3-from-scratch"
-echo "##################################"
-tigr-glimmer long-orfs -n -t 1.15 example.fa run1.longorfs
-tigr-glimmer extract -t example.fa run1.longorfs > run1.train
-tigr-glimmer build-icm -r run1.icm < run1.train
-tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run1.icm run1
-echo "=================================="
+echo 'Begin Test'
+/usr/lib/tigr-glimmer/long-orfs  -n -t 1.15 example.fa test1.longorfs
+/usr/lib/tigr-glimmer/extract -t example.fa test1.longorfs > test1.train
+/usr/lib/tigr-glimmer/build-icm -r test1.icm < test1.train
+/usr/lib/tigr-glimmer/glimmer3 example.fa test1.icm test1
+echo '---------------Passed!----------------------------'
 
-# for making this test, need fasta file with coords
-#echo "g3-from-training"
-#echo "##################################"
-#tigr-glimmer extract -t example.fa train.coords > run2.train
-#tigr-glimmer build-icm -r run2.icm < run2.train
-#tigr-glimmer upstream-coords.awk 25 0 train.coords | extract example.fa - > run2.upstream
-##elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
-##set startuse = ‘start-codon-distrib -3 example.fa train.coords‘
-##tigr-glimmer glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse example.fa run2.icm run2
-
-echo "g3-iterated"
-echo "##################################"
-tigr-glimmer long-orfs -n -t 1.15 example.fa run3.longorfs
-tigr-glimmer extract -t example.fa run3.longorfs > run3.train
-tigr-glimmer build-icm -r run3.icm < run3.train
-tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run3.icm run3.run1
-tail -n+2 run3.run1.predict > run3.coords
-# for making full test, need elph (elph not in repo)
-#upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
-#elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
-#set startuse = ‘start-codon-distrib -3 genom.seq run3.coords‘
-#tigr-glimmer glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
-echo "=================================="
-
-echo "PASS"



View it on GitLab: https://salsa.debian.org/med-team/tigr-glimmer/-/commit/12b2e3fae99d1de55b6464e820f0b40c0d32ea7c

-- 
View it on GitLab: https://salsa.debian.org/med-team/tigr-glimmer/-/commit/12b2e3fae99d1de55b6464e820f0b40c0d32ea7c
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