subject:"\[gentoo\-commits\] repo\/gentoo\:master commit in\: sci\-biology\/samtools\/, sci\-biology\/samtools\/files\/"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2020-08-03 Thread David Seifert

commit: b6948f3ed9612bc6f11b4ccab40ac4d80f73e397
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 21:11:18 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 21:11:18 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b6948f3e

sci-biology/samtools: Remove old

Closes: https://bugs.gentoo.org/728018
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest  |   2 -
 .../samtools/files/samtools-1.5-buildsystem.patch  | 413 -
 sci-biology/samtools/samtools-1.5.ebuild   |  61 ---
 sci-biology/samtools/samtools-1.9-r1.ebuild|  49 ---
 4 files changed, 525 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index b06f63a40e7..622e57502c3 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,4 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 
103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08
 SHA512 
828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
-DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 
1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023
 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
-DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 
409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff
 SHA512 
6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
deleted file mode 100644
index c466e66a9d1..000
--- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
+++ /dev/null
@@ -1,413 +0,0 @@
 a/config.mk.in
-+++ b/config.mk.in
-@@ -28,27 +28,26 @@
- # in the Makefile to reflect your configuration choices.  If you don't run
- # configure, the main Makefile contains suitable conservative defaults.
- 
--prefix   = @prefix@
--exec_prefix  = @exec_prefix@
--bindir   = @bindir@
--datarootdir  = @datarootdir@
--mandir   = @mandir@
-+prefix  = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir  = @bindir@
-+libdir  = @libdir@
-+datarootdir = @datarootdir@
-+mandir  = @mandir@
-+man1dir = $(mandir)/man1
- 
- CC   = @CC@
-+AR   = @AR@
- CPPFLAGS = @CPPFLAGS@
- CFLAGS   = @CFLAGS@
- LDFLAGS  = @LDFLAGS@
- LIBS = @LIBS@
- 
--@Hsource@HTSDIR = @HTSDIR@
--@Hsource@include $(HTSDIR)/htslib.mk
--@Hsource@include $(HTSDIR)/htslib_static.mk
--@Hsource@HTSLIB = $(HTSDIR)/libhts.a
--@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
--@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
--@Hsource@BGZIP = $(HTSDIR)/bgzip
--HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
--@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
--@Hinstall@HTSLIB_LIB = -lhts
-+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
-+HTSLIB_LIBS = @HTSLIB_LIBS@
- 
--CURSES_LIB = @CURSES_LIB@
-+NCURSES_CFLAGS = @NCURSES_CFLAGS@
-+NCURSES_LIBS = @NCURSES_LIBS@
-+
-+ZLIB_CFLAGS = @ZLIB_CFLAGS@
-+ZLIB_LIBS = @ZLIB_LIBS@
 a/configure.ac
-+++ b/configure.ac
-@@ -29,9 +29,6 @@
- AC_CONFIG_SRCDIR([bamtk.c])
- AC_CONFIG_HEADERS([config.h])
- 
--m4_include([m4/ax_with_curses.m4])
--m4_include([m4/ax_with_htslib.m4])
--
- dnl Copyright notice to be copied into the generated configure script
- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
- 
-@@ -39,73 +36,27 @@
- redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
- 
- AC_PROG_CC
-+AM_PROG_AR
- 
- AC_SYS_LARGEFILE
- 
--AX_WITH_HTSLIB
--if test "$ax_cv_htslib" != yes; then
--  AC_MSG_ERROR([HTSlib development files not found
--
--Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
--requires an unpacked HTSlib source tree (which will be built in conjunction
--with samtools) or a previously-installed HTSlib.  In either case you may
--need to configure --with-htslib=DIR to locate the appropriate HTSlib.
--
--FAILED.  You must supply an HTSlib in order to build samtools successfully.])
--fi
--
--if test "$ax_cv_htslib_which" = source; then
--  Hsource=
--  Hinstall='#'
--else
--  Hsource='#'
--  Hinstall=
--fi
--AC_SUBST([Hsource])
--AC_SUBST([Hinstall])
-+dnl htslib

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2017-09-02 Thread David Seifert

commit: d401db74e7e270ab7e38d955308cd8d2dbc20a48
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 09:30:07 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 09:32:42 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d401db74

sci-biology/samtools: Version bump to 1.5

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/samtools/Manifest  |   1 +
 .../samtools/files/samtools-1.5-buildsystem.patch  | 413 +
 sci-biology/samtools/samtools-1.5.ebuild   |  61 +++
 3 files changed, 475 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d25774fee86..791e2050ee7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -5,3 +5,4 @@ DIST samtools-1.0.tar.bz2 4459669 SHA256 
7340b843663c3f54a902a06f2f73c68198f3a62
 DIST samtools-1.1.tar.bz2 4495373 SHA256 
c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 
a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0
 WHIRLPOOL 
ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449
 DIST samtools-1.2.tar.bz2 4547126 SHA256 
420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 
4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d
 WHIRLPOOL 
273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4
 DIST samtools-1.3.tar.bz2 3978333 SHA256 
beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 
72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea
 WHIRLPOOL 
3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e
+DIST samtools-1.5.tar.bz2 4190142 SHA256 
8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
 WHIRLPOOL 
1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
new file mode 100644
index 000..248089e09fc
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
@@ -0,0 +1,413 @@
+--- a/config.mk.in
 b/config.mk.in
+@@ -28,27 +28,26 @@
+ # in the Makefile to reflect your configuration choices.  If you don't run
+ # configure, the main Makefile contains suitable conservative defaults.
+ 
+-prefix   = @prefix@
+-exec_prefix  = @exec_prefix@
+-bindir   = @bindir@
+-datarootdir  = @datarootdir@
+-mandir   = @mandir@
++prefix  = @prefix@
++exec_prefix = @exec_prefix@
++bindir  = @bindir@
++libdir  = @libdir@
++datarootdir = @datarootdir@
++mandir  = @mandir@
++man1dir = $(mandir)/man1
+ 
+ CC   = @CC@
++AR   = @AR@
+ CPPFLAGS = @CPPFLAGS@
+ CFLAGS   = @CFLAGS@
+ LDFLAGS  = @LDFLAGS@
+ LIBS = @LIBS@
+ 
+-@Hsource@HTSDIR = @HTSDIR@
+-@Hsource@include $(HTSDIR)/htslib.mk
+-@Hsource@include $(HTSDIR)/htslib_static.mk
+-@Hsource@HTSLIB = $(HTSDIR)/libhts.a
+-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
+-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+-@Hsource@BGZIP = $(HTSDIR)/bgzip
+-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
+-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
+-@Hinstall@HTSLIB_LIB = -lhts
++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
++HTSLIB_LIBS = @HTSLIB_LIBS@
+ 
+-CURSES_LIB = @CURSES_LIB@
++NCURSES_CFLAGS = @NCURSES_CFLAGS@
++NCURSES_LIBS = @NCURSES_LIBS@
++
++ZLIB_CFLAGS = @ZLIB_CFLAGS@
++ZLIB_LIBS = @ZLIB_LIBS@
+--- a/configure.ac
 b/configure.ac
+@@ -29,9 +29,6 @@
+ AC_CONFIG_SRCDIR([bamtk.c])
+ AC_CONFIG_HEADERS([config.h])
+ 
+-m4_include([m4/ax_with_curses.m4])
+-m4_include([m4/ax_with_htslib.m4])
+-
+ dnl Copyright notice to be copied into the generated configure script
+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
+ 
+@@ -39,73 +36,27 @@
+ redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
+ 
+ AC_PROG_CC
++AM_PROG_AR
+ 
+ AC_SYS_LARGEFILE
+ 
+-AX_WITH_HTSLIB
+-if test "$ax_cv_htslib" != yes; then
+-  AC_MSG_ERROR([HTSlib development files not found
+-
+-Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
+-requires an unpacked HTSlib source tree (which will be built in conjunction
+-with samtools) or a previously-installed HTSlib.  In either case you may
+-need to configure --with-htslib=DIR to locate the appropriate HTSlib.
+-
+-FAILED.  You must supply an HTSlib in order

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2016-03-27 Thread David Seifert

commit: deaa21ff2b928318d0e1b8fe45aa404411f08086
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 23:52:51 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 23:52:51 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=deaa21ff

sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions

Package-Manager: portage-2.2.28

 .../samtools/files/samtools-0.1.20-buildsystem.patch | 20 ++--
 ...tools-0.1.20.ebuild => samtools-0.1.20-r1.ebuild} |  2 +-
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
index dfdd890..eb9f693 100644
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
@@ -75,15 +75,15 @@
  .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
  
 -lib:libbam.a
-+lib:libbam-legacy.a
++lib:libbam-0.1-legacy.a
  
 -libbam.a:$(LOBJS)
-+libbam-legacy.a:$(LOBJS)
++libbam-0.1-legacy.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
  
  samtools:lib-recur $(AOBJS)
 -  $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools 
-lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam-legacy.a 
-Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
++  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy 
-Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
  
  razip:razip.o razf.o $(KNETFILE_O)
 -  $(CC) $(CFLAGS) -o $@ $^ -lz
@@ -105,21 +105,21 @@
  
 -libbam.1.dylib-local:$(LOBJS)
 -  libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-+libbam-legacy.1.dylib-local:$(LOBJS)
-+  libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz
++libbam-0.1-legacy.1.dylib-local:$(LOBJS)
++  libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz
  
 -libbam.so.1-local:$(LOBJS)
 -  $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc 
-lz
-+libbam-legacy.so.1-local:$(LOBJS)
-+  $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-legacy.so -o 
libbam-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
++libbam-0.1-legacy.so.1-local:$(LOBJS)
++  $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o 
libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
  
  dylib:
@$(MAKE) cleanlocal; \
case `uname` in \
 -  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam.so.1-local;; \
 -  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam.1.dylib-local;; \
-+  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-legacy.so.1-local;; \
-+  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-legacy.1.dylib-local;; \
++  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-0.1-legacy.so.1-local;; \
++  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-0.1-legacy.1.dylib-local;; \
*) echo 'Unknown OS';; \
esac
  
@@ -162,7 +162,7 @@
  
  bamcheck:bamcheck.o
 -  $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm 
-lbam-legacy -lpthread -lz
++  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm 
-lbam-0.1-legacy -lpthread -lz
  
  bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c

diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
similarity index 99%
rename from sci-biology/samtools/samtools-0.1.20.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r1.ebuild
index 3ee9956..744d15f 100644
--- a/sci-biology/samtools/samtools-0.1.20.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="http://samtools.sourceforge.net/;
 SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"
-SLOT="legacy"
+SLOT="0.1-legacy"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

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