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academic/STAR: Update Script.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Rob van Nues 2018-07-06 06:29:27 +07:00 committed by Willy Sudiarto Raharjo
parent bf5695bd8d
commit 7240d51d0c
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GPG key ID: 887B8374D7333381
4 changed files with 13 additions and 21 deletions
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6
academic/STAR/README
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@ -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

12
academic/STAR/STAR.SlackBuild
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@ -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

2
academic/STAR/STAR.info
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@ -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"

14
academic/STAR/reproducible.patch
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@ -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)