[med-svn] [Git][med-team/snpeff][master] 5 commits: Removing README.source about Mavenization
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Tue Feb 8 22:55:26 GMT 2022
Pierre Gruet pushed to branch master at Debian Med / snpeff
Commits:
7891daf0 by Pierre Gruet at 2022-02-06T20:55:01+01:00
Removing README.source about Mavenization
- - - - -
9a35e508 by Pierre Gruet at 2022-02-08T17:24:37+01:00
Refreshing classpath and dependencies
- - - - -
de0ec859 by Pierre Gruet at 2022-02-08T23:51:27+01:00
Having the conffile provided by libsnpeff-java instead of snpeff, as the lib itself now needs it
- - - - -
65451ea2 by Pierre Gruet at 2022-02-08T23:51:43+01:00
Adding autopkgtest
- - - - -
c2b3c1b3 by Pierre Gruet at 2022-02-08T23:53:11+01:00
Updating changelog
- - - - -
11 changed files:
- debian/README.Debian
- − debian/README.source
- debian/changelog
- debian/control
- + debian/libsnpeff-java.install
- + debian/libsnpeff-java.maintscript
- debian/libsnpeff-java.manifest
- debian/patches/update_launching_script_and_config_file_for_Debian.patch
- debian/snpeff.install
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.Debian
=====================================
@@ -1,13 +1,13 @@
When getting SnpEff from the upstream source repository, the configuration file
snpEff.config usually sits next to the jar; this is not the case for the Debian
packaging, because the jar is in /usr/share/java. So I am shipping a default
-/etc/snpEff.config file and it will be copied into ~/.snpEff/snpEff.config,
-which will be used, if the latter does not exist and if no other config file is
-given in the command line invocation.
+/etc/snpeff/snpEff.config file and it will be copied into
+~/.snpEff/snpEff.config, which will be used, if the latter does not exist and
+if no other config file is given in the command line invocation.
Moreover, by default data downloaded from the Internet by snpEff will be put
into ~/.snpEff/data. The users can change this by editing their per-user config
file ~/.snpEff/snpEff.config or by providing another config file on the command
line.
- -- Pierre Gruet <pgt at debian.org> Sun, 21 Feb 2021 15:45:10 +0100
+ -- Pierre Gruet <pgt at debian.org> Tue, 08 Feb 2022 23:44:18 +0100
=====================================
debian/README.source deleted
=====================================
@@ -1,9 +0,0 @@
-Information about snpeff
-------------------------
-
-This package was debianized using the mh_make command
-from the maven-debian-helper package.
-
-The build system uses Maven but prevents it from downloading
-anything from the Internet, making the build compliant with
-the Debian policy.
=====================================
debian/changelog
=====================================
@@ -4,16 +4,20 @@ snpeff (5.1+dfsg-1) UNRELEASED; urgency=medium
* Using tags instead of releases in d/watch
* Refreshing patches
* Refreshing d/copyright
- * Updating dependencies list and related Maven rules, notably switching
- to junit5
+ * Updating classpath, dependencies list and related Maven rules, notably
+ switching to junit5
* The path of the config file in the source has moved
* Using Debian-packaged biojava4 instead of biojava6, while upstream
previously used biojava3
* Disabling tests needing files that are not available
* Marking the doc package as Multi-Arch: foreign
* Adding a Lintian override for a file with very-long-lines
+ * Removing README.source about Mavenization
+ * Having the conffile provided by libsnpeff-java instead of snpeff, as the
+ lib itself now needs it
+ * Adding autopkgtest based on unit tests
- -- Pierre Gruet <pgt at debian.org> Sat, 29 Jan 2022 15:15:09 +0100
+ -- Pierre Gruet <pgt at debian.org> Tue, 08 Feb 2022 23:51:48 +0100
snpeff (4.3t+dfsg1-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -41,7 +41,9 @@ Rules-Requires-Root: no
Package: libsnpeff-java
Architecture: all
Depends: ${misc:Depends},
- ${maven:Depends}
+ ${maven:Depends},
+ libbiojava4-java,
+ libhtsjdk-java
Suggests: ${maven:OptionalDepends},
libsnpeff-java-doc
Description: genetic variant annotation and effect prediction toolbox - lib
=====================================
debian/libsnpeff-java.install
=====================================
@@ -0,0 +1 @@
+config/snpEff.config etc/snpeff
=====================================
debian/libsnpeff-java.maintscript
=====================================
@@ -0,0 +1,2 @@
+# Removing the conffile, which is now shipped in libsnpef-java
+mv_conffile /etc/snpEff.config /etc/snpeff/snpEff.config 5.1+dfsg-1~ snpeff
=====================================
debian/libsnpeff-java.manifest
=====================================
@@ -1,3 +1,3 @@
/usr/share/java/snpeff.jar:
- Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/log4j-1.2.jar /usr/share/java/biojava4-core.jar /usr/share/java/biojava4-structure.jar /usr/share/java/scala-library.jar
+ Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava4-core.jar /usr/share/java/biojava4-structure.jar
Main-Class: org.snpeff.SnpEff
=====================================
debian/patches/update_launching_script_and_config_file_for_Debian.patch
=====================================
@@ -1,14 +1,19 @@
-Description: Alter the launching script and the config file for a Debian install
+Description: Alter the launching script, the config file and relevant Java
+ files for a Debian install:
- Simplify the paths to account for a Debian installation.
- - Use the default /etc/snpEff.config file as configuration file if no file was
- given in the command line: it will be copied into ~/.snpEff/snpEff.config,
- which will be used as the configuration file is no other is given on the
- command line.
+ - Use the default /etc/snpeff/snpEff.config file as configuration file if no
+ file was given in the command line: it will be copied into
+ ~/.snpEff/snpEff.config, which will be used as the configuration file is no
+ other is given on the command line.
- By default, put data in ~/.snpEff/data.
- Correct bashisms in the launching script.
+ - In Config.java, use per-user config file if available. Else use the file in
+ /etc/snpeff. Else (which should normally just concern the unit tests), use
+ default file which should be in the source tree.
+ - Indicate path to effective config file in Java files.
Author: Pierre Gruet <pgt at debian.org>
Forwarded: not-needed
-Last-Update: 2021-02-21
+Last-Update: 2022-02-07
--- a/scripts/snpEff
+++ b/scripts/snpEff
@@ -49,7 +54,7 @@ Last-Update: 2021-02-21
+ fi
+
+ if [ -d ~/.snpEff -a ! -e ~/.snpEff/snpEff.config ]; then
-+ cp /etc/snpEff.config ~/.snpEff/snpEff.config
++ cp /etc/snpeff/snpEff.config ~/.snpEff/snpEff.config
+ fi
+
+ pass_args="$pass_args -c $HOME/.snpEff/snpEff.config"
@@ -69,3 +74,284 @@ Last-Update: 2021-02-21
#---
# Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')
+--- a/src/main/java/org/snpeff/PromoterSequences.java
++++ b/src/main/java/org/snpeff/PromoterSequences.java
+@@ -63,7 +63,7 @@
+ genes = new HashSet<Gene>();
+
+ Log.info("Loading database");
+- String configFile = HOME + "/snpEff/snpEff.config";
++ String configFile = HOME + "/.snpEff/snpEff.config";
+ config = new Config(genomeName, configFile);
+ config.loadSnpEffectPredictor();
+ snpEffectPredictor = config.getSnpEffectPredictor();
+--- a/src/main/java/org/snpeff/SnpEff.java
++++ b/src/main/java/org/snpeff/SnpEff.java
+@@ -163,7 +163,7 @@
+
+ public SnpEff() {
+ genomeVer = ""; // Genome version
+- configFile = Config.DEFAULT_CONFIG_FILE; // Config file
++ configFile = Config.defaultConfigFile(); // Config file
+ verbose = false; // Be verbose
+ debug = false; // Debug mode
+ quiet = false; // Be quiet
+--- a/src/main/java/org/snpeff/snpEffect/Config.java
++++ b/src/main/java/org/snpeff/snpEffect/Config.java
+@@ -16,6 +16,8 @@
+ public class Config implements Serializable, Iterable<String> {
+
+ public static final String DEFAULT_CONFIG_FILE = "snpEff.config";
++ public static final String ETC_CONFIG_FILE = "/etc/snpeff/snpEff.config";
++ public static final String PREFERRED_CONFIG_FILE = Gpr.HOME + "/.snpEff/snpEff.config";
+ public static final String DEFAULT_DATA_DIR = "./data";
+ // Keys in properties file
+ public static final String KEY_BUNDLE_SUFIX = ".bundle";
+@@ -94,7 +96,7 @@
+ * Create a config (uses DEFAULT_CONFIG_FILE)
+ */
+ public Config(String genomeVersion) {
+- init(genomeVersion, DEFAULT_CONFIG_FILE, null, null);
++ init(genomeVersion, defaultConfigFile(), null, null);
+ }
+
+ /**
+@@ -197,6 +199,23 @@
+ }
+ }
+
++ /**
++ * If Debian-preferred config file is available, give it.
++ * else, if the config file in /etc/snpeff is available, give it.
++ * Else, default to DEFAULT_CONFIG_FILE.
++ */
++ public static String defaultConfigFile() {
++ File preferred = new File(PREFERRED_CONFIG_FILE);
++ File etcFile = new File(ETC_CONFIG_FILE);
++ if (preferred.exists()) {
++ return PREFERRED_CONFIG_FILE;
++ } else if (etcFile.exists()) {
++ return ETC_CONFIG_FILE;
++ } else {
++ return DEFAULT_CONFIG_FILE;
++ }
++ }
++
+ /**
+ * Get a list of URLs that can be used to download a database
+ * Use compatible versions from 'getDatabaseCompatibilityVersions()'
+--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
++++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
+@@ -48,7 +48,7 @@
+ int totalOk = 0;
+ int totalWarnings = 0;
+ int totalNotFound = 0;
+- String configFile = Config.DEFAULT_CONFIG_FILE;
++ String configFile = Config.defaultConfigFile();
+ String proteinFile = "";
+ Map<String, String> proteinByTrId;
+ AutoHashMap<String, List<Transcript>> trByChromo;
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
+@@ -42,7 +42,7 @@
+ this.verbose = verbose;
+ this.snpEffectPredictor = snpEffectPredictor;
+ initRand();
+- config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
++ config = new Config("testCase", Config.defaultConfigFile());
+ }
+
+ public CompareEffects(String genomeName, long randSeed, boolean verbose) {
+@@ -50,7 +50,7 @@
+ this.randSeed = randSeed;
+ this.verbose = verbose;
+ initRand();
+- config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
++ config = new Config("testCase", Config.defaultConfigFile());
+ }
+
+ /**
+@@ -124,7 +124,7 @@
+
+ public void initSnpEffPredictor() {
+ // Create a config and force out snpPredictor for hg37 chromosome Y
+- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
++ config = new Config(genomeName, Config.defaultConfigFile());
+
+ if (snpEffectPredictor == null) {
+ config.loadSnpEffectPredictor();
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
+@@ -57,7 +57,7 @@
+ public CompareToEnsembl(String genomeName, boolean throwException) {
+ this.throwException = throwException;
+ if (verbose) Log.info("Loading predictor");
+- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
++ config = new Config(genomeName, Config.defaultConfigFile());
+ config.loadSnpEffectPredictor();
+ snpEffectPredictor = config.getSnpEffectPredictor();
+ genome = config.getGenome();
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
+@@ -33,7 +33,7 @@
+ */
+ public void run() {
+ Log.debug("Loading config files");
+- Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config("testCase", Config.defaultConfigFile());
+ config.loadSnpEffectPredictor();
+
+ for (Gene gint : config.getGenome().getGenes()) {
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
+@@ -75,7 +75,7 @@
+ */
+ protected void initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand) {
+ // Create a config and force out snpPredictor for hg37 chromosome Y
+- if (config == null) config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
++ if (config == null) config = new Config("testCase", Config.defaultConfigFile());
+
+ // Initialize factory
+ int maxGeneLen = 1000;
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
+@@ -95,7 +95,7 @@
+ String expectedResult = Gpr.readFile(resultFile).trim();
+
+ // Build
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryRefSeq factory = new SnpEffPredictorFactoryRefSeq(config);
+ factory.setFileName(refSeqFile);
+ factory.setVerbose(verbose);
+@@ -118,7 +118,7 @@
+ * Build a genome from a embl file and compare results to 'expected' results
+ */
+ public SnpEffectPredictor buildEmbl(String genome, String emblFile) {
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryEmbl sepEmbl = new SnpEffPredictorFactoryEmbl(config, emblFile);
+ SnpEffectPredictor sep = sepEmbl.create();
+ return sep;
+@@ -132,7 +132,7 @@
+ * Build a genome from a genbank file and compare results to 'expected' results
+ */
+ public SnpEffectPredictor buildGeneBank(String genome, String genBankFile, boolean circularCorrectlargeGap) {
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGenBank sepfg = new SnpEffPredictorFactoryGenBank(config, genBankFile);
+ sepfg.setVerbose(verbose);
+ sepfg.setCircularCorrectLargeGap(circularCorrectlargeGap);
+@@ -158,7 +158,7 @@
+ public SnpEffectPredictor buildGff3AndCompare(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) {
+
+ // Build
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGff3 fgff3 = new SnpEffPredictorFactoryGff3(config);
+ fgff3.setVerbose(verbose);
+ if (gff3File != null) fgff3.setFileName(gff3File);
+@@ -195,7 +195,7 @@
+ String expectedResult = Gpr.readFile(resultFile).trim();
+
+ // Build
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
+ fgtf22.setFileName(gtf22);
+ fgtf22.setVerbose(verbose);
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
+@@ -50,7 +50,7 @@
+ //---
+ // Load database and check some numbers
+ //---
+- String configFile = Config.DEFAULT_CONFIG_FILE;
++ String configFile = Config.defaultConfigFile();
+ Config config = new Config(genomeName, configFile);
+ if (verbose) Log.info("Loading database");
+ SnpEffectPredictor snpEffectPredictor = config.loadSnpEffectPredictor();
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
+@@ -281,7 +281,7 @@
+
+ // Load database
+ String genomeVer = "testHg3766Chr1";
+- config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);
++ config = new Config(genomeVer, Config.defaultConfigFile());
+ config.loadSnpEffectPredictor();
+ config.setTreatAllAsProteinCoding(true); // For historical reasons...
+ config.getSnpEffectPredictor().buildForest();
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
+@@ -25,7 +25,7 @@
+ // Load database
+ String genomeVer = "testHg3766Chr1";
+ Log.debug("Loading database '" + genomeVer + "'");
+- Config config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genomeVer, Config.defaultConfigFile());
+ config.setTreatAllAsProteinCoding(true); // For historical reasons...
+ config.loadSnpEffectPredictor();
+
+--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
+@@ -225,7 +225,7 @@
+ @Test
+ public void test_25_exon_bases() {
+ Log.debug("Test");
+- Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config("testCase", Config.defaultConfigFile());
+ config.loadSnpEffectPredictor();
+
+ String fastaFile = path("testCase.fa");
+@@ -283,7 +283,7 @@
+ String gtfFile = path("ENSMUSG00000005763.gtf");
+ String genome = "testMm37.61";
+
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
+ fgtf22.setFileName(gtfFile);
+ fgtf22.setReadSequences(false); // Don't read sequences
+--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
+@@ -254,7 +254,7 @@
+ protected void initSnpEffPredictor(Gene[] genesToAdd) {
+ // Create a config and force out snpPredictor
+ if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {
+- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
++ config = new Config(genomeName, Config.defaultConfigFile());
+ }
+
+ // Initialize factory
+--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
+@@ -44,7 +44,7 @@
+ protected void initSnpEffPredictor() {
+ // Create a config and force out snpPredictor
+ if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {
+- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
++ config = new Config(genomeName, Config.defaultConfigFile());
+ }
+
+ // Create predictor
+--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
++++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
+@@ -30,7 +30,7 @@
+ };
+
+ // Build
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);
+ sefGff.setFileName(gff);
+ sefGff.setVerbose(verbose);
+@@ -68,7 +68,7 @@
+ };
+
+ // Build
+- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
++ Config config = new Config(genome, Config.defaultConfigFile());
+ SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);
+ sefGff.setFileName(gff);
+ sefGff.setFastaFile(fasta);
=====================================
debian/snpeff.install
=====================================
@@ -1,2 +1 @@
scripts/snpEff usr/bin
-config/snpEff.config etc
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: default-jdk-headless, junit5, libsnpeff-java, quilt
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,36 @@
+#!/bin/bash
+set -e
+
+pkg=snpeff
+
+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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+# Push patches if some of them still have to be applied, but don't fail else.
+QUILT_PATCHES="debian/patches" quilt push -a || true
+
+# Copying config file in home dir.
+HOME="$(mktemp -d)"
+echo "xxxxxxxx $HOME";
+echo "xxxxxxxx $(readlink -f ~)";
+mkdir -p ~/.snpEff
+cp /etc/snpeff/snpEff.config ~/.snpEff
+
+mkdir -p "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
+cp -a src/main/java/org/snpeff/snpEffect/testCases/integration "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
+cp -a src/main/java/org/snpeff/snpEffect/testCases/unity "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
+cp -a tests/ "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+mkdir classes/
+
+javac -d classes -cp /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava4-core.jar:/usr/share/java/biojava4-sequencing.jar:/usr/share/java/biojava4-structure.jar org/snpeff/snpEffect/testCases/*/*.java
+
+# Only running unit tests, not integration ones (needing data from the Internet)
+java -jar /usr/share/java/junit-platform-console-standalone.jar --class-path /usr/share/java/snpeff.jar:/usr/share/java/biojava4-sequencing.jar:classes --select-package org.snpeff.snpEffect.testCases.unity
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023
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