[med-svn] [tophat] 01/03: remove convenience copy of samtools

Fabian Klötzl kloetzl-guest at moszumanska.debian.org
Mon Dec 4 13:05:12 UTC 2017 

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kloetzl-guest pushed a commit to branch master
in repository tophat.

commit ab81542a5e21b5ad0043d76e6c44e65c893a1585
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Mon Dec 4 12:30:53 2017 +0100

    remove convenience copy of samtools
    
    Closes #780816
---
 debian/patches/hardening4samtools.patch            |  21 --
 .../remove-convenience-copy-of-samtools.patch      | 224 +++++++++++++++++++++
 debian/patches/series                              |   2 +-
 3 files changed, 225 insertions(+), 22 deletions(-)

diff --git a/debian/patches/hardening4samtools.patch b/debian/patches/hardening4samtools.patch
deleted file mode 100644
index 83d1570..0000000
--- a/debian/patches/hardening4samtools.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Don't overwrite CFLAGS, add CPPFLAGS and LDFLAGS fot the embedded
-copy of samtools
-Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
---- tophat.orig/src/samtools-0.1.18/Makefile
-+++ tophat/src/samtools-0.1.18/Makefile
-@@ -1,5 +1,5 @@
- CC=			gcc
--CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-+
- DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
- KNETFILE_O=	knetfile.o
- LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -41,7 +41,7 @@
- 		$(AR) -csru $@ $(LOBJS)
- 
- samtools_0.1.18:lib-recur $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
-+		$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz $(LDFLAGS) #$(LIBCURSES)
- 
- razip:razip.o razf.o $(KNETFILE_O)
- 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
diff --git a/debian/patches/remove-convenience-copy-of-samtools.patch b/debian/patches/remove-convenience-copy-of-samtools.patch
new file mode 100644
index 0000000..0f84111
--- /dev/null
+++ b/debian/patches/remove-convenience-copy-of-samtools.patch
@@ -0,0 +1,224 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 4 Dec 2017 12:28:43 +0100
+Subject: remove convenience copy of samtools
+
+---
+ configure.ac | 10 ----
+ src/Makefile.am | 125 ++++++--------------------------------------------------
+ 2 files changed
+
+diff --git a/src/Makefile.am b/src/Makefile.am
+index e983fee..986e321 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -16,90 +16,6 @@ sortedcontainers/sorteddict.py \
+ sortedcontainers/sortedlist.py \
+ sortedcontainers/sortedlistwithkey.py \
+ sortedcontainers/sortedset.py \
+-samtools-0.1.18/AUTHORS \
+-samtools-0.1.18/COPYING \
+-samtools-0.1.18/ChangeLog \
+-samtools-0.1.18/INSTALL \
+-samtools-0.1.18/Makefile \
+-samtools-0.1.18/Makefile.mingw \
+-samtools-0.1.18/NEWS \
+-samtools-0.1.18/bam.c \
+-samtools-0.1.18/bam.h \
+-samtools-0.1.18/bam2bcf.c \
+-samtools-0.1.18/bam2bcf.h \
+-samtools-0.1.18/bam2bcf_indel.c \
+-samtools-0.1.18/bam2depth.c \
+-samtools-0.1.18/bam_aux.c \
+-samtools-0.1.18/bam_cat.c \
+-samtools-0.1.18/bam_color.c \
+-samtools-0.1.18/bam_endian.h \
+-samtools-0.1.18/bam_import.c \
+-samtools-0.1.18/bam_index.c \
+-samtools-0.1.18/bam_lpileup.c \
+-samtools-0.1.18/bam_mate.c \
+-samtools-0.1.18/bam_md.c \
+-samtools-0.1.18/bam_pileup.c \
+-samtools-0.1.18/bam_plcmd.c \
+-samtools-0.1.18/bam_reheader.c \
+-samtools-0.1.18/bam_rmdup.c \
+-samtools-0.1.18/bam_rmdupse.c \
+-samtools-0.1.18/bam_sort.c \
+-samtools-0.1.18/bam_stat.c \
+-samtools-0.1.18/bam_tview.c \
+-samtools-0.1.18/bamtk.c \
+-samtools-0.1.18/bedidx.c \
+-samtools-0.1.18/bgzf.c \
+-samtools-0.1.18/bgzf.h \
+-samtools-0.1.18/bgzip.c \
+-samtools-0.1.18/cut_target.c \
+-samtools-0.1.18/errmod.c \
+-samtools-0.1.18/errmod.h \
+-samtools-0.1.18/faidx.c \
+-samtools-0.1.18/faidx.h \
+-samtools-0.1.18/kaln.c \
+-samtools-0.1.18/kaln.h \
+-samtools-0.1.18/khash.h \
+-samtools-0.1.18/klist.h \
+-samtools-0.1.18/knetfile.c \
+-samtools-0.1.18/knetfile.h \
+-samtools-0.1.18/kprobaln.c \
+-samtools-0.1.18/kprobaln.h \
+-samtools-0.1.18/kseq.h \
+-samtools-0.1.18/ksort.h \
+-samtools-0.1.18/kstring.c \
+-samtools-0.1.18/kstring.h \
+-samtools-0.1.18/phase.c \
+-samtools-0.1.18/razf.c \
+-samtools-0.1.18/razf.h \
+-samtools-0.1.18/razip.c \
+-samtools-0.1.18/sam.c \
+-samtools-0.1.18/sam.h \
+-samtools-0.1.18/sam_header.c \
+-samtools-0.1.18/sam_header.h \
+-samtools-0.1.18/sam_view.c \
+-samtools-0.1.18/sample.c \
+-samtools-0.1.18/sample.h \
+-samtools-0.1.18/samtools.1 \
+-samtools-0.1.18/bcftools/Makefile \
+-samtools-0.1.18/bcftools/README \
+-samtools-0.1.18/bcftools/bcf.c \
+-samtools-0.1.18/bcftools/bcf.h \
+-samtools-0.1.18/bcftools/bcf.tex \
+-samtools-0.1.18/bcftools/bcf2qcall.c \
+-samtools-0.1.18/bcftools/bcfutils.c \
+-samtools-0.1.18/bcftools/call1.c \
+-samtools-0.1.18/bcftools/em.c \
+-samtools-0.1.18/bcftools/fet.c \
+-samtools-0.1.18/bcftools/index.c \
+-samtools-0.1.18/bcftools/kfunc.c \
+-samtools-0.1.18/bcftools/kmin.c \
+-samtools-0.1.18/bcftools/kmin.h \
+-samtools-0.1.18/bcftools/main.c \
+-samtools-0.1.18/bcftools/mut.c \
+-samtools-0.1.18/bcftools/prob1.c \
+-samtools-0.1.18/bcftools/prob1.h \
+-samtools-0.1.18/bcftools/vcf.c \
+-samtools-0.1.18/bcftools/vcfutils.pl \
+ SeqAn-1.4.2/LICENSE \
+ SeqAn-1.4.2/README.rst \
+ SeqAn-1.4.2/seqan/align/align_base.h \
+@@ -683,17 +599,11 @@ SeqAn-1.4.2/seqan/system/system_sema.h \
+ SeqAn-1.4.2/seqan/system/system_thread.h \
+ SeqAn-1.4.2/seqan/version.h
+ 
+-SAMDIR = ./samtools-0.1.18
+-SAMLIB = libbam.a
+-SAMPROG = samtools_0.1.18
+ BAM_LIB = -lbam
+-BAM_CPPFLAGS = -I$(SAMDIR)
+-BAM_LDFLAGS = -L$(SAMDIR)
+ 
+ #-- progs to be installed in $prefix/bin
+ 
+ bin_PROGRAMS = \
+-	$(SAMPROG) \
+ 	prep_reads \
+ 	gtf_to_fasta \
+ 	fix_map_ordering \
+@@ -732,7 +642,7 @@ tophat: tophat.py
+ 	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
+ 
+ #-- tophat library for linking convienence
+-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
++noinst_LIBRARIES = libgc.a libtophat.a
+ 
+ noinst_HEADERS = \
+ 	reads.h \
+@@ -798,58 +708,49 @@ libgc_a_SOURCES = \
+ 
+ prep_reads_SOURCES = prep_reads.cpp
+ prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) 
++prep_reads_LDFLAGS = $(LDFLAGS) 
+ 
+ segment_juncs_SOURCES = segment_juncs.cpp
+ segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
++segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+ long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
++long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+ gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++gtf_juncs_LDFLAGS = $(LDFLAGS)
+ 
+ juncs_db_SOURCES = juncs_db.cpp
+ juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++juncs_db_LDFLAGS = $(LDFLAGS)
+ 
+ tophat_reports_SOURCES = tophat_reports.cpp
+ tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
++tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+ fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++fix_map_ordering_LDFLAGS = $(LDFLAGS)
+ 
+ bam2fastx_SOURCES = bam2fastx.cpp
+ bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam2fastx_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++bam2fastx_LDFLAGS = $(LDFLAGS)
+ 
+ bam_merge_SOURCES = bam_merge.cpp
+ bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam_merge_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++bam_merge_LDFLAGS = $(LDFLAGS)
+ 
+ sam_juncs_SOURCES = sam_juncs.cpp
+ sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-sam_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++sam_juncs_LDFLAGS = $(LDFLAGS)
+ 
+ map2gtf_SOURCES = map2gtf.cpp
+ map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-map2gtf_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++map2gtf_LDFLAGS = $(LDFLAGS)
+ 
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+ gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
++gtf_to_fasta_LDFLAGS = $(LDFLAGS)
+ 
+-
+-libbam_a_SOURCES = 
+-samtools_0_1_18_SOURCES = 
+-
+-$(SAMPROG): $(SAMLIB)
+-	
+-
+-$(SAMLIB):
+-	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
+
+diff --git a/configure.ac b/configure.ac
+index dd5ac83..1a7f32b 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -38,16 +38,6 @@ if test -z "$BOOST_THREAD_LIBS"; then
+ fi
+ 
+ 
+-# BAM related:
+- ac_bam_path=samtools-0.1.18
+- BAM_LIB="-lbam"
+- BAM_LDFLAGS="-L./$ac_bam_path"
+- BAM_CPPFLAGS="-I./$ac_bam_path"
+- AC_SUBST(BAM_CPPFLAGS)
+- AC_SUBST(BAM_LDFLAGS)
+- AC_SUBST(BAM_LIB)
+-
+-
+ # Checks for header files.
+ AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 5ad469c..32c87aa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
-hardening4samtools.patch
 remove_3rd_party_code.patch
 fix_includes_path.patch
 fix-gcc6.patch
+remove-convenience-copy-of-samtools.patch

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