Package: drop-seq / 3.0.2+dfsg-1

Metadata

Package Version Patches format
drop-seq 3.0.2+dfsg-1 3.0 (quilt)

Patch series

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

src/ant/defs.xml | 5 0 + 5 - 0 !
1 file changed, 5 deletions(-)

 do not try to run git
debian_packaged_libs.patch | (download)

src/ant/defs.xml | 4 4 + 0 - 0 !
1 file changed, 4 insertions(+)

 use debian packaged java libs
link_excluded_file.patch | (download)

README.md | 4 1 + 3 - 0 !
1 file changed, 1 insertion(+), 3 deletions(-)

 the pdf documentation had to be excluded as binary without source
 This patch links to the online version
paths_in_scripts.patch | (download)

src/scripts/defs.sh | 7 1 + 6 - 0 !
1 file changed, 1 insertion(+), 6 deletions(-)

 putting debian paths for the jars in .sh executables
no_google_api_gax.patch | (download)

src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/ClassifyDropSeqFunctionalData.java | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 com.google.api.gax.rpc is not packaged in debian
openjdk_21_syntax.patch | (download)

src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DataProcessorUtils.java | 2 1 + 1 - 0 !
src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqPriorityScore.java | 22 14 + 8 - 0 !
src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloPriorityScore.java | 19 12 + 7 - 0 !
src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/ClassifyDropSeqFunctionalData.java | 4 2 + 2 - 0 !
src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/OptimusDropSeqLocusFunctionComparison.java | 4 2 + 2 - 0 !
src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java | 2 1 + 1 - 0 !
src/java/org/broadinstitute/dropseqrna/beadsynthesis/CountBarcodeSequences.java | 2 1 + 1 - 0 !
src/java/org/broadinstitute/dropseqrna/utils/readiterators/GeneFunctionProcessor.java | 6 3 + 3 - 0 !
src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.java | 6 3 + 3 - 0 !
src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqFunctionalDataProcessorTest.java | 4 2 + 2 - 0 !
src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloFunctionalDataProcessorTest.java | 6 3 + 3 - 0 !
11 files changed, 44 insertions(+), 33 deletions(-)

 some pieces of syntax are for openjdk-21, which is not yet the
 default one in Debian. Let's remove this patch when it is.
put_defs_sh_out_of_path.patch | (download)

src/scripts/Drop-seq_alignment.sh | 2 1 + 1 - 0 !
src/scripts/create_Drop-seq_reference_metadata.sh | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 putting defs.sh under /usr/share/drop-seq-tools in order to avoid
 such a classic and short name in /usr/bin