Add autopkgtests
Nilesh Patra
3 years ago
0 | 0 | #!/bin/bash |
1 | 1 | set -e |
2 | 2 | |
3 | pkg="tigr-glimmer" | |
3 | pkg=tigr-glimmer | |
4 | 4 | |
5 | if [ "$AUTOPKGTEST_TMP" = "" ] ; then | |
5 | if [ "${AUTOPKGTEST_TMP}" = "" ] ; then | |
6 | 6 | AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) |
7 | trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM | |
7 | trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM | |
8 | 8 | fi |
9 | 9 | |
10 | cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP | |
10 | cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" | |
11 | 11 | |
12 | cd $AUTOPKGTEST_TMP | |
13 | find . -name "*.gz" -exec gunzip \{\} \; | |
12 | cd "${AUTOPKGTEST_TMP}" | |
13 | gunzip -r * | |
14 | 14 | |
15 | echo "g3-from-scratch" | |
16 | echo "##################################" | |
17 | tigr-glimmer long-orfs -n -t 1.15 example.fa run1.longorfs | |
18 | tigr-glimmer extract -t example.fa run1.longorfs > run1.train | |
19 | tigr-glimmer build-icm -r run1.icm < run1.train | |
20 | tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run1.icm run1 | |
21 | echo "==================================" | |
15 | echo 'Begin Test' | |
16 | /usr/lib/tigr-glimmer/long-orfs -n -t 1.15 example.fa test1.longorfs | |
17 | /usr/lib/tigr-glimmer/extract -t example.fa test1.longorfs > test1.train | |
18 | /usr/lib/tigr-glimmer/build-icm -r test1.icm < test1.train | |
19 | /usr/lib/tigr-glimmer/glimmer3 example.fa test1.icm test1 | |
20 | echo '---------------Passed!----------------------------' | |
22 | 21 | |
23 | # for making this test, need fasta file with coords | |
24 | #echo "g3-from-training" | |
25 | #echo "##################################" | |
26 | #tigr-glimmer extract -t example.fa train.coords > run2.train | |
27 | #tigr-glimmer build-icm -r run2.icm < run2.train | |
28 | #tigr-glimmer upstream-coords.awk 25 0 train.coords | extract example.fa - > run2.upstream | |
29 | ##elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif | |
30 | ##set startuse = ‘start-codon-distrib -3 example.fa train.coords‘ | |
31 | ##tigr-glimmer glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse example.fa run2.icm run2 | |
32 | ||
33 | echo "g3-iterated" | |
34 | echo "##################################" | |
35 | tigr-glimmer long-orfs -n -t 1.15 example.fa run3.longorfs | |
36 | tigr-glimmer extract -t example.fa run3.longorfs > run3.train | |
37 | tigr-glimmer build-icm -r run3.icm < run3.train | |
38 | tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run3.icm run3.run1 | |
39 | tail -n+2 run3.run1.predict > run3.coords | |
40 | # for making full test, need elph (elph not in repo) | |
41 | #upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream | |
42 | #elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif | |
43 | #set startuse = ‘start-codon-distrib -3 genom.seq run3.coords‘ | |
44 | #tigr-glimmer glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3 | |
45 | echo "==================================" | |
46 | ||
47 | echo "PASS" |