Nilesh Patra pushed to branch master at Debian Med / alter-sequence-alignment
Commits: cb6b5e03 by Nilesh Patra at 2020-11-16T16:34:49+05:30 Add autopkgtests - - - - - 74542cab by Nilesh Patra at 2020-11-16T16:35:12+05:30 routine-update: Standards-Version: 4.5.0 - - - - - a409cf3d by Nilesh Patra at 2020-11-16T16:35:12+05:30 routine-update: debhelper-compat 13 - - - - - e2d16f13 by Nilesh Patra at 2020-11-16T16:35:22+05:30 routine-update: Add salsa-ci file - - - - - 6c81a9fb by Nilesh Patra at 2020-11-16T16:35:22+05:30 routine-update: Rules-Requires-Root: no - - - - - cfe0b324 by Nilesh Patra at 2020-11-16T16:35:34+05:30 Set upstream metadata fields: Bug-Submit. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html - - - - - 22073afa by Nilesh Patra at 2020-11-16T11:42:28+00:00 Set CLASSPATH - - - - - f4e1fb17 by Nilesh Patra at 2020-11-16T11:42:56+00:00 Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - + debian/salsa-ci.yml - + debian/tests/control - + debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,19 @@ +alter-sequence-alignment (1.3.4-4) unstable; urgency=medium + + * Team Upload. + [ Andreas Tille ] + * Remove substvars + + [ Nilesh Patra ] + * Add autopkgtests + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Submit. + + -- Nilesh Patra <[email protected]> Mon, 16 Nov 2020 16:35:35 +0530 + alter-sequence-alignment (1.3.4-3) unstable; urgency=medium * Replace python-markdown by markdown ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: java Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), javahelper, maven-debian-helper, libproperties-maven-plugin-java, @@ -13,10 +13,11 @@ Build-Depends: debhelper-compat (= 12), libargs4j-java, rename, markdown -Standards-Version: 4.4.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/alter-sequence-alignment Vcs-Git: https://salsa.debian.org/med-team/alter-sequence-alignment.git Homepage: http://sing.ei.uvigo.es/ALTER/ +Rules-Requires-Root: no Package: alter-sequence-alignment Architecture: all ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, default-jdk +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,88 @@ +#!/bin/bash +set -e + +pkg="alter-sequence-alignment" +CUR_DIR=`pwd` + +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 ${CUR_DIR}/alter-lib/src/main/java/* $AUTOPKGTEST_TMP +cp -a ${CUR_DIR}/alter-web/src/main/resources/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP +gunzip -r * + +echo "Test 1" +alter-sequence-alignment -i muscle.aln -ia -of FASTA -oo Linux -op MUSCLE -o test1 +[ -s test1 ] || exit 1 +rm -f ./test1 +echo "PASS" + +echo "Test 2" +alter-sequence-alignment -i tcoffee.aln -ia -of MSF -oo Linux -op TCoffee -o test2 +[ -s test2 ] || exit 1 +rm -f ./test2 +echo "PASS" + +echo "Test converter" +cat >TestAlter.java <<HERE +import es.uvigo.ei.sing.alter.converter.Converter; +import es.uvigo.ei.sing.alter.converter.DefaultFactory; +import es.uvigo.ei.sing.alter.parser.ParseException; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Paths; + +public class TestAlter { + + public static void main(String[] args) throws IOException { + Converter converter = new DefaultFactory().getConverter( + "Linux", // Input operating system (Linux, MacOS or Windows) + "clustal", // Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee) + "NEXUS", // Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR) + false, // Autodetect format (other input options are omitted) + false, // Collapse sequences to haplotypes + true, // Treat gaps as missing data when collapsing + false, // Count missing data as differences when collapsing + 0, // Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0) + "windows", // Output operating system (Linux, MacOS or Windows) + "general", // Output program (jModelTest, MrBayes, PAML, PAUP, PhyML, + // ProtTest, RAxML, TCS, CodABC, + // BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT, + // MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL) + "aln", // Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR) + false, // Low case output + false, // Output residue numbers (only ALN format) + false, // Sequential output (only NEXUS and PHYLIP formats) + false, // Output match characters + "MyConverterApp" // identifier for log messages + ); + + + try { + String inputSequence = new String(Files.readAllBytes(Paths.get("clustal.nex"))); + + String converted = converter.convert(inputSequence); + + System.out.println("converted file:"); + System.out.println(converted); + + } catch (ParseException e) { + System.err.println("the input file seems to contain errors"); + e.printStackTrace(); + } + + } +} + +HERE + +CLASSPATH=".:/usr/share/java/alter-lib.jar:/usr/share/java/alter.jar" +javac TestAlter.java +java TestAlter +rm -f ./TestAlter* +echo "PASS" ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,4 @@ +Bug-Submit: https://github.com/sing-group/ALTER/issues/new Reference: Author: > Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08 -- View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
