Package: artemis / 18.1.0+dfsg-3

Metadata

Package Version Patches format
artemis 18.1.0+dfsg-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
samreader.patch | (download)

src/main/java/uk/ac/sanger/artemis/components/alignment/BamUtils.java | 22 11 + 11 - 0 !
1 file changed, 11 insertions(+), 11 deletions(-)

 implement new htsjdk api
 See https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
use lang3.patch | (download)

src/main/java/uk/ac/sanger/artemis/io/GFF3Encoder.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use lang3
using_system_jars_in_pom.patch | (download)

pom.xml | 6 6 + 0 - 0 !
1 file changed, 6 insertions(+)

 specifying paths on debian system for some dependencies
 For those dependencies, no maven-repo tree is available, we are therefore
 giving their path with system scope.
missing_htsjdk_dependency_in_pom.patch | (download)

pom.xml | 8 7 + 1 - 0 !
1 file changed, 7 insertions(+), 1 deletion(-)

 adding missing dependency on htsjdk in pom
no_install_of_provided_jars.patch | (download)

pom.xml | 70 0 + 70 - 0 !
1 file changed, 70 deletions(-)

 avoid installing embedded jars as we removed them
 Author relies on jars that are embedded in their source archive. Instead, we
 use the ones that are packaged in Debian.
running_build_tests.patch | (download)

pom.xml | 27 3 + 24 - 0 !
src/test/java/uk/ac/sanger/artemis/components/variant/WriteVCFTest.java | 2 1 + 1 - 0 !
src/test/java/uk/ac/sanger/artemis/components/variant/WriteVariantSitesTest.java | 7 6 + 1 - 0 !
3 files changed, 10 insertions(+), 26 deletions(-)

 changes in pom and in test definitions when they cannot be run
 In pom.xml, we remove the part relative to Evosuite as, as mentioned in pom,
 provided build tests are not compatible with Evosuite.
 We also remove the lines allowing to skip tests or to ignore failures.
 In the definitions of the tests, we add @Ignore for the ones that require a
 X11 instance to run.
debianize_launcher_scripts.patch | (download)

act | 62 1 + 61 - 0 !
art | 62 1 + 61 - 0 !
bamview | 60 1 + 59 - 0 !
dnaplotter | 63 1 + 62 - 0 !
4 files changed, 4 insertions(+), 243 deletions(-)

 simplifying the provided launchers
 Many options or tricks are useless on a Debian system.
 The paths are also adapted to the Debian install.