[med-svn] [Git][med-team/artemis][master] 6 commits: Keeping the etc folder in the jars
Pierre Gruet
gitlab at salsa.debian.org
Sun Sep 6 21:44:55 BST 2020
Pierre Gruet pushed to branch master at Debian Med / artemis
Commits:
2e4fdc5f by Pierre Gruet at 2020-09-06T21:35:39+02:00
Keeping the etc folder in the jars
- - - - -
08f28709 by Pierre Gruet at 2020-09-06T21:39:30+02:00
Fixing insecure uri and trailing whitespaces in debian/control
- - - - -
56101fc2 by Pierre Gruet at 2020-09-06T22:41:48+02:00
Replacing symlinks to jars with upstream-provided scripts
- - - - -
d6a8bdc7 by Pierre Gruet at 2020-09-06T22:42:23+02:00
Adapting the provided launchers scripts to Debian systems
- - - - -
3699617e by Pierre Gruet at 2020-09-06T22:43:01+02:00
Updating and completing manpages of act and dnaplotter
- - - - -
57794f7c by Pierre Gruet at 2020-09-06T22:44:41+02:00
Updating changelog
- - - - -
10 changed files:
- debian/artemis.install
- − debian/artemis.links
- − debian/bin/bamview
- debian/changelog
- debian/control
- debian/man/act.1
- debian/man/dnaplotter.1
- + debian/patches/debianize_launcher_scripts.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/artemis.install
=====================================
@@ -3,4 +3,7 @@ target/modifiedJars/act.jar usr/share/java/
target/modifiedJars/bamview.jar usr/share/java/
target/modifiedJars/dnaplotter.jar usr/share/java/
debian/desktop/*.desktop usr/share/applications/
-debian/bin usr
+act usr/bin
+art usr/bin
+bamview usr/bin
+dnaplotter usr/bin
=====================================
debian/artemis.links deleted
=====================================
@@ -1,3 +0,0 @@
-usr/share/java/artemis.jar usr/bin/art
-usr/share/java/act.jar usr/bin/act
-usr/share/java/dnaplotter.jar usr/bin/dnaplotter
=====================================
debian/bin/bamview deleted
=====================================
@@ -1,10 +0,0 @@
-#! /bin/sh -e
-
-# export JAVA_HOME=/usr/lib/jvm/default-java
-export JAVA_CMD=java
-jarname=/usr/share/java/$(basename $0).jar
-
-# Include the wrappers utility script
-. /usr/lib/java-wrappers/java-wrappers.sh
-
-run_java -jar $jarname "$@"
=====================================
debian/changelog
=====================================
@@ -21,8 +21,11 @@ artemis (18.1.0+dfsg-1) UNRELEASED; urgency=medium
* Updating dependencies as Maven now replaces ant for the build
* Updating debian/copyright as paths have changed
* Building with Maven instead of ant
+ * Fixing insecure uri and trailing whitespaces in debian/control
+ * Replacing symlinks to jars with upstream-provided scripts
+ * Updating and completing manpages of act and dnaplotter
- -- Pierre Gruet <pgtdebian at free.fr> Sun, 06 Sep 2020 15:24:56 +0200
+ -- Pierre Gruet <pgtdebian at free.fr> Sun, 06 Sep 2020 22:43:16 +0200
artemis (17.0.1+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -37,7 +37,7 @@ Build-Depends: debhelper-compat (= 13),
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/artemis
Vcs-Git: https://salsa.debian.org/med-team/artemis.git
-Homepage: http://www.sanger.ac.uk/science/tools/artemis
+Homepage: https://www.sanger.ac.uk/science/tool/artemis
Rules-Requires-Root: no
Package: artemis
@@ -64,7 +64,7 @@ Depends: ${misc:Depends},
Description: genome browser and annotation tool
Artemis is a genome browser and annotation tool that allows visualisation of
sequence features, next generation data and the results of analyses within the
- context of the sequence, and also its six-frame translation.
+ context of the sequence, and also its six-frame translation.
.
This package includes the Artemis genome browser, the Artemis Comparison
Tool (ACT), and the DNAplotter and BamView utilities.
=====================================
debian/man/act.1
=====================================
@@ -1,6 +1,38 @@
-.TH ACT 1 "October 2015"
+.TH ACT 1 "September 2020"
.SH NAME
act \- Artemis comparison tool for genome sequences
+
+.SH SYNOPSIS
+.B act
+.RI [ options ]
+.I SEQUENCE_1
+.I COMPARISON_1_2
+.I SEQUENCE_2
+.I ...
+
+.SH OPTIONS
+ SEQUENCE An EMBL, GenBank, FASTA, or GFF3 file
+ FEATURE An Artemis TAB file, or GFF file
+ COMPARISON A BLAST comparison file in tabular format
+
+ -options FILE Read a text file of options from FILE
+ -chado Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)
+
+ -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
+ -DuserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots
+ -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)
+ -DbamX=FILE[,FILE2,...] For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files
+ -Dchado="h:p/d?u" Get ACT to open this CHADO database
+ -Dread_only Open CHADO database read-only
+
+.SH EXAMPLES
+ % act
+ % act af063097.embl af063097_v_b132222.crunch b132222.embl
+ % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
+ % act -Duserplot2=/pathToFile/userPlot
+
.SH SEE ALSO
+ http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
+
.BR art (1),
.BR dnaplotter (1)
=====================================
debian/man/dnaplotter.1
=====================================
@@ -1,6 +1,20 @@
-.TH DNAPLOTTER 1 "October 2015"
+.TH DNAPLOTTER 1 "September 2020"
.SH NAME
dnaplotter \- make circular plots of genomes
+
+.SH SYNOPSIS
+.B dnaplotter
+.RI [ options ]
+
+.SH OPTIONS
+ -t FILE Read a template file
+
+.SH EXAMPLES
+ % dnaplotter
+ % dnaplotter -t <template-file>
+
.SH SEE ALSO
+ http://www.sanger.ac.uk/science/tools/dnaplotter/
+
.BR art (1),
.BR act (1)
=====================================
debian/patches/debianize_launcher_scripts.patch
=====================================
@@ -0,0 +1,360 @@
+Description: Simplifying the provided launchers
+ Many options or tricks are useless on a Debian system.
+ The paths are also adapted to the Debian install.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: not-needed
+Last-Update: 2020-09-06
+
+--- a/act
++++ b/act
+@@ -38,36 +38,6 @@
+ exit 0
+ }
+
+-add_proxy_properties() {
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_PROXY
+- fi
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_proxy
+- fi
+-
+- if [[ "$http_proxy" != "" ]]
+- then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+- fi
+-}
+-
+-#
+-# Resolve script path (inc symlinks)
+-#
+-SOURCE="${BASH_SOURCE[0]}"
+-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+- SOURCE="$(readlink "$SOURCE")"
+- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+-done
+-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
+-
+-
+ # Special Sanger override on chado PGUSER
+ if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
+ then
+@@ -93,28 +63,6 @@
+ shift
+ done
+
+-
+-JAR_NAME=act.jar
+-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
+-
+-#
+-# Use a custom Java version if necessary
+-#
+-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
+-then
+- JAVA=`which java`
+-else
+- JAVA_HOME=$ARTEMIS_JAVA_JRE
+- JAVA=$ARTEMIS_JAVA_JRE/bin/java
+-fi
+-
+-#
+-# Allow URLs to work from behind firewalls.
+-#
+-add_proxy_properties
+-
+ #
+ # "-mx2g" sets the maximum amount of memory to use.
+ # This may need to be increased when dealing with large files
+@@ -132,20 +80,12 @@
+ #
+ FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
+
+-PLATTMP=`uname`
+-if [[ "$PLATTMP" = "Darwin" ]]
+-then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=ACT"
+- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
+-fi
+-
+ if [[ "$QUIET" = no ]]
+ then
+ echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
+ fi
+
+-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*
++java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/act.jar $*
+ result=$?
+
+ exit $result
+--- a/art
++++ b/art
+@@ -44,36 +44,6 @@
+ exit 0
+ }
+
+-add_proxy_properties() {
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_PROXY
+- fi
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_proxy
+- fi
+-
+- if [[ "$http_proxy" != "" ]]
+- then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+- fi
+-}
+-
+-#
+-# Resolve script path (inc symlinks)
+-#
+-SOURCE="${BASH_SOURCE[0]}"
+-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+- SOURCE="$(readlink "$SOURCE")"
+- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+-done
+-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
+-
+-
+ # Special Sanger override on chado PGUSER
+ if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
+ then
+@@ -99,28 +69,6 @@
+ shift
+ done
+
+-
+-JAR_NAME=artemis.jar
+-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
+-
+-#
+-# Use a custom Java version if necessary
+-#
+-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
+-then
+- JAVA=`which java`
+-else
+- JAVA_HOME=$ARTEMIS_JAVA_JRE
+- JAVA=$ARTEMIS_JAVA_JRE/bin/java
+-fi
+-
+-#
+-# Allow URLs to work from behind firewalls.
+-#
+-add_proxy_properties
+-
+ #
+ # "-mx2g" sets the maximum amount of memory to use.
+ # This may need to be increased when dealing with large files
+@@ -139,20 +87,12 @@
+ #
+ FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
+
+-PLATTMP=`uname`
+-if [[ "$PLATTMP" = "Darwin" ]]
+-then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis"
+- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
+-fi
+-
+ if [[ "$QUIET" = "no" ]]
+ then
+ echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
+ fi
+
+-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*
++java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/artemis.jar $*
+ result=$?
+
+ exit $result
+--- a/bamview
++++ b/bamview
+@@ -6,57 +6,7 @@
+
+ QUIET=no
+
+-add_proxy_properties() {
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_PROXY
+- fi
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_proxy
+- fi
+-
+- if [[ "$http_proxy" != "" ]]
+- then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+- fi
+-}
+-
+-#
+-# Resolve script path (inc symlinks)
+-#
+-SOURCE="${BASH_SOURCE[0]}"
+-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+- SOURCE="$(readlink "$SOURCE")"
+- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+-done
+-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
+-
+-
+ APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
+-JAR_NAME=bamview.jar
+-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
+-
+-#
+-# Use a custom Java version if necessary
+-#
+-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
+-then
+- JAVA=`which java`
+-else
+- JAVA_HOME=$ARTEMIS_JAVA_JRE
+- JAVA=$ARTEMIS_JAVA_JRE/bin/java
+-fi
+-
+-#
+-# Allow URLs to work from behind firewalls.
+-#
+-add_proxy_properties
+
+ #
+ # "-mx2g" sets the maximum amount of memory to use.
+@@ -69,20 +19,12 @@
+ FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
+ fi
+
+-PLATTMP=`uname`
+-if [[ "$PLATTMP" = "Darwin" ]]
+-then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
+- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
+-fi
+-
+ if [[ "$QUIET" = "no" ]]
+ then
+ echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
+ fi
+
+-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
++java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/bamview.jar $*
+ result=$?
+
+ exit $result
+--- a/dnaplotter
++++ b/dnaplotter
+@@ -25,37 +25,6 @@
+ exit 0
+ }
+
+-add_proxy_properties() {
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_PROXY
+- fi
+-
+- if [[ "$http_proxy" = "" ]]
+- then
+- http_proxy=$HTTP_proxy
+- fi
+-
+- if [[ "$http_proxy" != "" ]]
+- then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+- fi
+-}
+-
+-
+-#
+-# Resolve script path (inc symlinks)
+-#
+-SOURCE="${BASH_SOURCE[0]}"
+-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+- SOURCE="$(readlink "$SOURCE")"
+- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+-done
+-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
+-
+-
+ #
+ # Parse arguments.
+ #
+@@ -75,28 +44,6 @@
+ shift
+ done
+
+-
+-JAR_NAME=dnaplotter.jar
+-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
+-
+-#
+-# Use a custom Java version if necessary
+-#
+-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
+-then
+- JAVA=`which java`
+-else
+- JAVA_HOME=$ARTEMIS_JAVA_JRE
+- JAVA=$ARTEMIS_JAVA_JRE/bin/java
+-fi
+-
+-#
+-# Allow URLs to work from behind firewalls.
+-#
+-add_proxy_properties
+-
+ #
+ # "-mx2g" sets the maximum amount of memory to use.
+ # This may need to be increased when dealing with large files
+@@ -108,20 +55,12 @@
+ FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
+ fi
+
+-PLATTMP=`uname`
+-if [[ "$PLATTMP" = "Darwin" ]]
+-then
+- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"
+- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
+-fi
+-
+ if [[ "$QUIET" = "no" ]]
+ then
+ echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
+ fi
+
+-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
++java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/dnaplotter.jar $TEMPLATE_FILE_ARG
+ result=$?
+
+ exit $result
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ using_system_jars_in_pom.patch
missing_htsjdk_dependency_in_pom.patch
no_install_of_provided_jars.patch
running_build_tests.patch
+debianize_launcher_scripts.patch
=====================================
debian/rules
=====================================
@@ -40,7 +40,7 @@ override_dh_auto_build:
# but we don't use it since it creates shaded jars.
cd target/ && mkdir jarsBuild && mkdir modifiedJars && cd jarsBuild && \
jar xf ../artemis-*.jar && \
- $(RM) -rf etc/ META_INF/ && \
+ $(RM) -rf META_INF/ && \
jar cf artemis.jar * && \
mv artemis.jar ../modifiedJars/ && \
cp ../modifiedJars/artemis.jar ../modifiedJars/act.jar && \
View it on GitLab: https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c
--
View it on GitLab: https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c
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