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
|