Import tophat-2.1.1 as wip/tophat.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Import tophat-2.1.1 as wip/tophat.
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 15:26:53 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 10:26:53 2016 -0500
Changeset:	f93b6b393abf75ca8912351ae2b5e32634ba93ec

Added Files:
	tophat/DESCR
	tophat/Makefile
	tophat/PLIST
	tophat/TODO
	tophat/distinfo
	tophat/patches/patch-src-bam_merge.cpp
	tophat/patches/patch-src-samtools-0.1.18-Makefile
	tophat/patches/patch-src_Makefile.in

Log Message:
Import tophat-2.1.1 as wip/tophat.

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f93b6b393abf75ca8912351ae2b5e32634ba93ec

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 tophat/DESCR                                      |  4 +++
 tophat/Makefile                                   | 40 +++++++++++++++++++++++
 tophat/PLIST                                      | 29 ++++++++++++++++
 tophat/TODO                                       |  1 +
 tophat/distinfo                                   |  9 +++++
 tophat/patches/patch-src-bam_merge.cpp            | 10 ++++++
 tophat/patches/patch-src-samtools-0.1.18-Makefile | 28 ++++++++++++++++
 tophat/patches/patch-src_Makefile.in              | 23 +++++++++++++
 8 files changed, 144 insertions(+)

diffs:
diff --git a/tophat/DESCR b/tophat/DESCR
new file mode 100644
index 0000000..5ec85b9
--- /dev/null
+++ b/tophat/DESCR
@@ -0,0 +1,4 @@
+TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
+reads to mammalian-sized genomes using the ultra high-throughput short read
+aligner Bowtie, and then analyzes the mapping results to identify splice
+junctions between exons.
diff --git a/tophat/Makefile b/tophat/Makefile
new file mode 100644
index 0000000..ddd1394
--- /dev/null
+++ b/tophat/Makefile
@@ -0,0 +1,40 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Mar  3 09:54:03 CST 2016               #
+###########################################################
+
+DISTNAME=	tophat-${PORTVERSION}
+CATEGORIES=	biology
+# Note: Distfiles on Github are not the same as those here
+MASTER_SITES=	http://ccb.jhu.edu/software/tophat/downloads/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://ccb.jhu.edu/software/tophat/index.shtml
+COMMENT=	Fast splice junction mapper for RNA-Seq reads
+LICENSE=	boost-license
+
+MAKE_JOBS_SAFE=	no
+
+DEPENDS+=	bowtie2>=0:../../wip/bowtie2
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+GNU_CONFIGURE=	yes
+
+REPLACE_PYTHON=	src/bed_to_juncs \
+		src/contig_to_chr_coords \
+		src/sra_to_solid \
+		src/tophat-fusion-post \
+		src/tophat.py
+REPLACE_BASH=	src/tophat2.sh
+
+CFLAGS+=	-Wno-unused
+
+PORTVERSION=	2.1.1
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/tophat/PLIST b/tophat/PLIST
new file mode 100644
index 0000000..96f3f27
--- /dev/null
+++ b/tophat/PLIST
@@ -0,0 +1,29 @@
+@comment $NetBSD$
+bin/bam2fastx
+bin/bam_merge
+bin/bed_to_juncs
+bin/contig_to_chr_coords
+bin/fix_map_ordering
+bin/gtf_juncs
+bin/gtf_to_fasta
+bin/intervaltree/__init__.py
+bin/intervaltree/interval.py
+bin/intervaltree/intervaltree.py
+bin/intervaltree/node.py
+bin/juncs_db
+bin/long_spanning_reads
+bin/map2gtf
+bin/prep_reads
+bin/sam_juncs
+bin/samtools_0.1.18
+bin/segment_juncs
+bin/sortedcontainers/__init__.py
+bin/sortedcontainers/sorteddict.py
+bin/sortedcontainers/sortedlist.py
+bin/sortedcontainers/sortedlistwithkey.py
+bin/sortedcontainers/sortedset.py
+bin/sra_to_solid
+bin/tophat
+bin/tophat2
+bin/tophat-fusion-post
+bin/tophat_reports
diff --git a/tophat/TODO b/tophat/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/tophat/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/tophat/distinfo b/tophat/distinfo
new file mode 100644
index 0000000..fcc01d0
--- /dev/null
+++ b/tophat/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+SHA1 (tophat-2.1.1.tar.gz) = 33e81e57528520edd3e67bf2259e1f3a30998a3b
+RMD160 (tophat-2.1.1.tar.gz) = 73c06278ad8bddacc3c83f1dd7f7da6e7dd148c2
+SHA512 (tophat-2.1.1.tar.gz) = e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
+Size (tophat-2.1.1.tar.gz) = 2259554 bytes
+SHA1 (patch-src-bam_merge.cpp) = 3fd585b5e1d15a3c4d42dbc152852b44bb1c6dbf
+SHA1 (patch-src-samtools-0.1.18-Makefile) = 54dfa3947fb260b2936050b1b2229a785febb327
+SHA1 (patch-src_Makefile.in) = 50aac2d59688ec99c9c6b315b79f832bf2218bd2
diff --git a/tophat/patches/patch-src-bam_merge.cpp b/tophat/patches/patch-src-bam_merge.cpp
new file mode 100644
index 0000000..aef0c40
--- /dev/null
+++ b/tophat/patches/patch-src-bam_merge.cpp
@@ -0,0 +1,10 @@
+$NetBSD$
+
+# Missing header
+--- src/bam_merge.cpp.orig	2016-02-14 18:21:17.113079000 +0000
++++ src/bam_merge.cpp
+@@ -1,3 +1,4 @@
++#include <getopt.h>
+ #include "bam_merge.h"
+ 
+ #define USAGE "Usage: bam_merge [-Q] <out.bam> <in1.bam> <in2.bam> [...]\n"
diff --git a/tophat/patches/patch-src-samtools-0.1.18-Makefile b/tophat/patches/patch-src-samtools-0.1.18-Makefile
new file mode 100644
index 0000000..ce2fb39
--- /dev/null
+++ b/tophat/patches/patch-src-samtools-0.1.18-Makefile
@@ -0,0 +1,28 @@
+$NetBSD$
+
+# Respect build environment
+--- src/samtools-0.1.18/Makefile.orig	2016-02-14 18:21:17.376079000 +0000
++++ src/samtools-0.1.18/Makefile
+@@ -1,5 +1,10 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
++CC?=			gcc
++CFLAGS?=		-g -Wall -O2 #-m64 #-arch ppc
++CC?=           gcc
++CFLAGS?=       -g -Wall -O2
++# Link fails with clang on inlined functions with no -O
++CFLAGS+=       -O
++RANLIB?=       ranlib
+ 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	\
+@@ -38,7 +43,8 @@ all:$(PROG)
+ lib:libbam.a
+ 
+ libbam.a:$(LOBJS)
+-		$(AR) -csru $@ $(LOBJS)
++		$(AR) cr $@ $(LOBJS)
++		$(RANLIB) $@
+ 
+ samtools_0.1.18:lib-recur $(AOBJS)
+ 		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
diff --git a/tophat/patches/patch-src_Makefile.in b/tophat/patches/patch-src_Makefile.in
new file mode 100644
index 0000000..e3a1f0c
--- /dev/null
+++ b/tophat/patches/patch-src_Makefile.in
@@ -0,0 +1,23 @@
+$NetBSD$
+
+# Allow pkgsrc to control make program
+--- src/Makefile.in.orig	2016-02-24 03:08:32.568707000 +0000
++++ src/Makefile.in
+@@ -1658,7 +1658,7 @@ uninstall-am: uninstall-binPROGRAMS unin
+ 
+ 
+ clean-local:
+-	cd $(SAMDIR) && make clean
++	cd $(SAMDIR) && ${MAKE} clean
+ 
+ tophat2: tophat2.sh
+ 	cp tophat2.sh tophat2 && chmod 755 tophat2
+@@ -1669,7 +1669,7 @@ tophat: tophat.py
+ $(SAMPROG): $(SAMLIB)
+ 
+ $(SAMLIB):
+-	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
++	cd $(SAMDIR) && ${MAKE} $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
+ 
+ install-data-hook:
+ 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)
Follow-Ups:
- Re: Import tophat-2.1.1 as wip/tophat.
  - From: Thomas Klausner
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