Pierre Gruet pushed to branch master at Debian Med / snpeff
Commits: 6d58a59d by Pierre Gruet at 2021-02-21T22:49:36+01:00 Putting config file and downloaded data in a dot directory by default - - - - - 5 changed files: - debian/README.Debian - debian/changelog - debian/manpages/snpEff.1 - debian/patches/series - debian/patches/update_launching_script_for_Debian.patch → debian/patches/update_launching_script_and_config_file_for_Debian.patch Changes: ===================================== debian/README.Debian ===================================== @@ -1,4 +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.config, which will be used, if the latter does not exist and if no other config file is given in the command line invocation. +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. - -- Pierre Gruet <[email protected]> Fri, 19 Feb 2021 09:22:13 +0100 +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 <[email protected]> Sun, 21 Feb 2021 15:45:10 +0100 ===================================== debian/changelog ===================================== @@ -4,8 +4,11 @@ snpeff (4.3t+dfsg-1) UNRELEASED; urgency=medium TODO: - Ensure upstream provides files with proper copyrighting and licensing. - fill in debian/copyright, maybe remove the html/ folder. - - check my patch replacing akka with java.util.concurrent. - snpsift is to package elsewhere on its own. - - add autopkgtest + - add autopkgtest if possible, as many many tasks need downloading data + from the Internet before. + - Find out where the build date is recorded and stored (it is then + outputted as shown, for instance, in the example from the website) to + allow for build reproducibility. -- Pierre Gruet <[email protected]> Fri, 19 Feb 2021 09:47:24 +0100 ===================================== debian/manpages/snpEff.1 ===================================== @@ -59,7 +59,7 @@ Create a translocations report (from VCF file). .SS "Generic options" .TP \fB\-c\fR , \fB\-config\fR -Specify config file +Specify config file. Default: ~/.snpEff/snpEff.config .TP \fB\-configOption\fR name=value Override a config file option ===================================== debian/patches/series ===================================== @@ -4,4 +4,4 @@ adapting_to_htsjdk.patch adding_scala_in_pom.patch fix_tests.patch alter_pom_for_debian_packaging.patch -update_launching_script_for_Debian.patch +update_launching_script_and_config_file_for_Debian.patch ===================================== debian/patches/update_launching_script_for_Debian.patch → debian/patches/update_launching_script_and_config_file_for_Debian.patch ===================================== @@ -1,12 +1,14 @@ -Description: Alter the launching script fora Debian installation +Description: Alter the launching script and the config filefor 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.config, which will - be used as the config file is no other is given on the command line. - - Correct bashisms. + 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. Author: Pierre Gruet <[email protected]> Forwarded: not-needed -Last-Update: 2021-02-19 +Last-Update: 2021-02-21 --- a/scripts/snpEff +++ b/scripts/snpEff @@ -31,7 +33,7 @@ Last-Update: 2021-02-19 default_jvm_mem_opts="-Xms1g -Xmx4g" jvm_mem_opts="" -@@ -39,12 +33,16 @@ +@@ -39,12 +33,20 @@ esac done @@ -42,13 +44,28 @@ Last-Update: 2021-02-19 -if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then - pass_args="$pass_args -c ${jardir}/snpEff.config" +if [ "$pass_args" != "" ] && ! echo "$pass_args" | grep "\-c " ; then -+ if [ ! -e ~/.snpEff.config ]; then -+ cp /etc/snpEff.config ~/.snpEff.config ++ if [ ! -d ~/.snpEff ]; then ++ mkdir ~/.snpEff + fi + -+ pass_args="$pass_args -c $HOME/.snpEff.config" ++ if [ -d ~/.snpEff -a ! -e ~/.snpEff/snpEff.config ]; then ++ cp /etc/snpEff.config ~/.snpEff/snpEff.config ++ fi ++ ++ pass_args="$pass_args -c $HOME/.snpEff/snpEff.config" fi -exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args +exec java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpeff.jar $pass_args exit +--- a/snpEff.config ++++ b/snpEff.config +@@ -14,7 +14,7 @@ + # Also, a non-absolute path will be relative to config's file dir + # + #--- +-data.dir = ./data/ ++data.dir = ~/.snpEff/data/ + + #--- + # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54 -- View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54 You're receiving this email because of your account on salsa.debian.org.
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