diff options
| author | Rob van Nues <sborg63@disroot.org> | 2018-07-06 06:29:27 +0700 |
|---|---|---|
| committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2018-07-07 06:54:17 +0700 |
| commit | 7240d51d0c1534f9b7b73458b29159dee1fb6329 (patch) | |
| tree | 8d13c79eb1fa4d21e8d8064bb3e33b39a5dc66e4 /academic | |
| parent | bf5695bd8d62f073d40b8750eeb6361481ff7ea9 (diff) | |
academic/STAR: Update Script.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/STAR/README | 6 | ||||
| -rw-r--r-- | academic/STAR/STAR.SlackBuild | 12 | ||||
| -rw-r--r-- | academic/STAR/STAR.info | 2 | ||||
| -rw-r--r-- | academic/STAR/reproducible.patch | 14 |
4 files changed, 13 insertions, 21 deletions
diff --git a/academic/STAR/README b/academic/STAR/README index 3608afef93cb0..24272d0a1f558 100644 --- a/academic/STAR/README +++ b/academic/STAR/README @@ -1,7 +1,7 @@ STAR aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays, resulting in fast, accurate mapping. -STAR is capable of unbiased de novo detection of canonical junctions, -can discover non-canonical splices and chimeric (fusion) transcripts and -can map full-length RNA sequences. +STAR is capable of unbiased de novo detection of canonical splice +junctions, can discover non-canonical splices and chimeric (fusion) +transcripts and can map full-length RNA sequences. Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index aa89b2927f9c0..d6f0453abe39d 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -63,9 +63,15 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# https://sources.debian.org/data/main/r/rna-star/2.6.0b+dfsg-1/debian/patches/reproducible.patch -# (with minor modification) -patch -p1 < $CWD/reproducible.patch +# for using shared, externally-installed htslib (as done on debian) +#rm -rf htslib +# from https://salsa.debian.org/med-team/rna-star/tree/master/debian/patches +#patch < $CWD/donotuse_own_htslib.patch + +# but Alex Dobin, the developer of STAR does not advise this due to hacks he made in htslib +# https://github.com/alexdobin/STAR/issues/351 +# https://github.com/alexdobin/STAR/issues/447 +#so let's forget about this for now cd source diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 2ba024dafd8f3..a5a7a64b311b0 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.6.0c/STAR-2.6.0c.ta MD5SUM_x86_64="014e44faa78c13e781bb74d9b5cf00d8" REQUIRES="" MAINTAINER="Rob van Nues" -EMAIL="rvnues { at } disroot { dot } org" +EMAIL="sborg63@disroot.org" diff --git a/academic/STAR/reproducible.patch b/academic/STAR/reproducible.patch deleted file mode 100644 index f340376023b4a..0000000000000 --- a/academic/STAR/reproducible.patch +++ /dev/null @@ -1,14 +0,0 @@ -Description: make build reproducible - Stops build hostname and directory from being recorded in the artifact. -Author: Sascha Steinbiss <sascha@steinbiss.name> ---- a/source/Makefile -+++ b/source/Makefile -@@ -18,7 +18,7 @@ - LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a - LDFLAGS_gdb += $(LDFLAGS_shared) - --COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"' -+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="<unrecorded>"' - - CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add) - CXXFLAGS_main += -O3 $(CXXFLAGS_common) |