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

2023-05-05 Thread David Seifert 
commit: f8ed4029d610b62eb95b85692efd9396ab8fd933
Author: David Seifert  gentoo  org>
AuthorDate: Fri May  5 09:19:58 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri May  5 09:19:58 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f8ed4029

sci-biology/samtools: drop 0.1.20-r4

Closes: https://bugs.gentoo.org/862288
Signed-off-by: David Seifert  gentoo.org>

 profiles/package.mask  |   6 -
 sci-biology/samtools/Manifest  |   1 -
 .../files/samtools-0.1.20-buildsystem.patch| 206 -
 sci-biology/samtools/samtools-0.1.20-r4.ebuild |  73 
 4 files changed, 286 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f381e12c4b19..5b737647d95d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -283,12 +283,6 @@ dev-ruby/allison
 # Removal on 2023-05-07.  Bug #878655.
 app-misc/wildq
 
-# David Seifert  (2023-04-06)
-# Last release over 7 years ago, abandoned upstream, still depends on
-# dead 0.1-legacy samtools slot. No revdeps in tree.
-# Removal on 2023-05-06. Bug #862288.
-sci-biology/samtools:0.1-legacy
-
 # Ionen Wolkens  (2023-03-30)
 # NVIDIA dropped support for the 390.xx branch in December 2022[1].
 #

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 5787a3bb63e6..72408c9c9544 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1 @@
-DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 
09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260
 SHA512 
107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3

diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
deleted file mode 100644
index eb9f6934a96f..
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ /dev/null
@@ -1,206 +0,0 @@
 samtools-0.1.20/bcftools/Makefile
-+++ samtools-0.1.20/bcftools/Makefile
-@@ -1,6 +1,6 @@
--CC=   gcc
--CFLAGS=   -g -Wall -O2 #-m64 #-arch ppc
--DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-+CC?=  gcc
-+CFLAGS?=  -g -Wall -O2 #-m64 #-arch ppc
-+CPPFLAGS+=-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
- LOBJS=bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o 
index.o fet.o mut.o bcf2qcall.o
- OMISC=..
- AOBJS=call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o 
$(OMISC)/knetfile.o $(OMISC)/bedidx.o
-@@ -11,14 +11,14 @@
- .SUFFIXES:.c .o
- 
- .c.o:
--  $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
-+  $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
- 
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
-   @target=`echo $@ | sed s/-recur//`; \
-   wdir=`pwd`; \
-   list='$(SUBDIRS)'; for subdir in $$list; do \
-   cd $$subdir; \
--  $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" 
CFLAGS="$(CFLAGS)" \
-+  $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" 
CFLAGS="$(CFLAGS)" \
-   INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" 
$$target || exit 1; \
-   cd $$wdir; \
-   done;
-@@ -31,7 +31,7 @@
-   $(AR) -csru $@ $(LOBJS)
- 
- bcftools:lib $(AOBJS)
--  $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz 
-lpthread
-+  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf 
-lm -lz -lpthread
- 
- bcf.o:bcf.h
- vcf.o:bcf.h
 samtools-0.1.20/Makefile
-+++ samtools-0.1.20/Makefile
-@@ -4,10 +4,10 @@
- #   make git-stamp
- VERSION=
- 
--CC=   gcc
--CFLAGS=   -g -Wall $(VERSION) -O2
--#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
--DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 
-D_USE_KNETFILE -D_CURSES_LIB=1
-+CC?=  gcc
-+CFLAGS?=  -g -Wall $(VERSION) -O2
-+#LDFLAGS+=-Wl,-rpath,\$$ORIGIN/../lib
-+CPPFLAGS+=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE 
-D_CURSES_LIB=1
- KNETFILE_O=   knetfile.o
- LOBJS=bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o 
bam_index.o \
-   bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o 
bedidx.o \
-@@ -28,14 +28,14 @@
- .PHONY: all lib
- 
- .c.o:
--  $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+  $(CC)

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

2017-09-02 Thread David Seifert 
commit: 06dc3754671e25127fa53a7d8b6c17ab3d254e40
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 15:01:47 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 15:02:09 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06dc3754

sci-biology/samtools: Add missing -I. to CPPFLAGS

Bug: https://bugs.gentoo.org/show_bug.cgi?id=629666
Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/samtools/files/samtools-1.5-buildsystem.patch | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
index 248089e09fc..c466e66a9d1 100644
--- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
+++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
@@ -196,7 +196,7 @@
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
  
 +$(LOBJS):
-+  $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
++  $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<
 +
  
  LIBST_OBJS = sam_opts.o sam_utils.o

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

2017-09-02 Thread David Seifert 
commit: 70386b8c804f2bf2fb7aca4be74d511d765ad1e4
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 11:07:41 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:37:02 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70386b8c

sci-biology/samtools: Remove old

Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170
Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618
Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593

 sci-biology/samtools/Manifest  |   6 -
 .../files/samtools-0.1.19-buildsystem.patch| 183 -
 .../samtools/files/samtools-1.0-buildsystem.patch  |  59 --
 .../samtools/files/samtools-1.1-buildsystem.patch  | 153 -
 .../samtools/files/samtools-1.2-buildsystem.patch  | 193 --
 .../samtools/files/samtools-1.3-buildsystem.patch  | 174 -
 .../samtools/files/samtools-1.3-ncurses.patch  | 737 -
 sci-biology/samtools/samtools-0.1.12.ebuild|  30 -
 sci-biology/samtools/samtools-0.1.19-r2.ebuild |  60 --
 sci-biology/samtools/samtools-1.0-r1.ebuild|  72 --
 sci-biology/samtools/samtools-1.0.ebuild   |  68 --
 sci-biology/samtools/samtools-1.1.ebuild   |  82 ---
 sci-biology/samtools/samtools-1.2.ebuild   |  82 ---
 sci-biology/samtools/samtools-1.3-r1.ebuild|  96 ---
 14 files changed, 1995 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 791e2050ee7..a1c0aa6b427 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,8 +1,2 @@
-DIST samtools-0.1.12a.tar.bz2 355633 SHA256 
377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 
8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012
 WHIRLPOOL 
da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c
-DIST samtools-0.1.19.tar.bz2 514507 SHA256 
d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 
d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d
 WHIRLPOOL 
7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5
 DIST samtools-0.1.20.tar.gz 566387 SHA256 
500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 WHIRLPOOL 
3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0
-DIST samtools-1.0.tar.bz2 4459669 SHA256 
7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 
5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693
 WHIRLPOOL 
2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832
-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-0.1.19-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
deleted file mode 100644
index d5ff3bd45da..000

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

2016-03-28 Thread David Seifert 
commit: 767b616524e6b171ed4775fe35ecd068f58abc22
Author: David Seifert  gentoo  org>
AuthorDate: Mon Mar 28 19:59:02 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Mar 28 19:59:24 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=767b6165

sci-biology/samtools: version bump to 1.3, to match htslib

* EAPI=6
* Added modern AX_WITH_CURSES that works with pkg-config
* Fixed incorrect symlinks for libbam.so

Package-Manager: portage-2.2.28

 sci-biology/samtools/Manifest  |   1 +
 .../samtools/files/samtools-1.3-buildsystem.patch  | 174 +
 .../samtools/files/samtools-1.3-ncurses.patch  | 737 +
 sci-biology/samtools/samtools-1.3.ebuild   |  86 +++
 4 files changed, 998 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index fd88ba4..d25774f 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -4,3 +4,4 @@ DIST samtools-0.1.20.tar.gz 566387 SHA256 
500019b4d1886ad995513d5ce8b413b14b51f1
 DIST samtools-1.0.tar.bz2 4459669 SHA256 
7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 
5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693
 WHIRLPOOL 
2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832
 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

diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
new file mode 100644
index 000..61f6b03
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
@@ -0,0 +1,174 @@
+--- samtools-1.3/Makefile
 samtools-1.3/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC   = gcc
+-CPPFLAGS =
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
+-LIBS =
++CC   ?= gcc
++CPPFLAGS +=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  +=
++LIBS +=
++BAMLIB   ?= libbam.a
+ 
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+ LOBJS=  bam_aux.o bam.o bam_import.o sam.o \
+@@ -42,6 +43,7 @@
+ prefix  = /usr/local
+ exec_prefix = $(prefix)
+ bindir  = $(exec_prefix)/bin
++libdir ?= $(exec_prefix)/lib
+ datarootdir = $(prefix)/share
+ mandir  = $(datarootdir)/man
+ man1dir = $(mandir)/man1
+@@ -129,67 +131,74 @@
+ .c.o:
+   $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+ 
++$(LOBJS):
++  $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+ 
+-lib:libbam.a
++lib:libbam.a libbam.so.1.0
+ 
+ libbam.a:$(LOBJS)
+   $(AR) -csru $@ $(LOBJS)
+ 
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+-  $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) 
$(CURSES_LIB) -lm $(ALL_LIBS)
++libbam.so.1.0:$(LOBJS)
++  $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++  ln -sf $@ libbam.so.1
++  ln -sf $@ libbam.so
++
++samtools: $(AOBJS) lib
++  $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) 
$(LIBCURSES) -lm -lz
+ 
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) 
$(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) 
$(bam2bcf_h) $(bam_lpileup_h)
+ sam_h = sam.h $(htslib_sam_h) $(bam_h)
+ sam_opts_h = sam_opts.h $(htslib_hts_h)
+-sample_h = sample.h $(htslib_kstring_h)
++sample_h = sample.h
+ 
+ bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h)

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

2016-03-27 Thread David Seifert 
commit: f7caa54d3afffe8220d1a5f237b8906a994a0792
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:39:22 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:58 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7caa54d

sci-biology/samtools: Version bump to 0.1.20

* EAPI=6
* samtools will be slotted with SLOT="legacy", in order
  to be able to install applications that rely on the old
  monolithic library.

Package-Manager: portage-2.2.28

 sci-biology/samtools/Manifest  |   1 +
 .../files/samtools-0.1.20-buildsystem.patch| 206 +
 sci-biology/samtools/samtools-0.1.20.ebuild|  64 +++
 3 files changed, 271 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index dae2fbd..fd88ba4 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,5 +1,6 @@
 DIST samtools-0.1.12a.tar.bz2 355633 SHA256 
377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 
8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012
 WHIRLPOOL 
da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c
 DIST samtools-0.1.19.tar.bz2 514507 SHA256 
d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 
d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d
 WHIRLPOOL 
7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5
+DIST samtools-0.1.20.tar.gz 566387 SHA256 
500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 WHIRLPOOL 
3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0
 DIST samtools-1.0.tar.bz2 4459669 SHA256 
7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 
5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693
 WHIRLPOOL 
2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832
 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

diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
new file mode 100644
index 000..dfdd890
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
@@ -0,0 +1,206 @@
+--- samtools-0.1.20/bcftools/Makefile
 samtools-0.1.20/bcftools/Makefile
+@@ -1,6 +1,6 @@
+-CC=   gcc
+-CFLAGS=   -g -Wall -O2 #-m64 #-arch ppc
+-DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
++CC?=  gcc
++CFLAGS?=  -g -Wall -O2 #-m64 #-arch ppc
++CPPFLAGS+=-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS=bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o 
index.o fet.o mut.o bcf2qcall.o
+ OMISC=..
+ AOBJS=call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o 
$(OMISC)/knetfile.o $(OMISC)/bedidx.o
+@@ -11,14 +11,14 @@
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+-  $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
++  $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
+ 
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+   @target=`echo $@ | sed s/-recur//`; \
+   wdir=`pwd`; \
+   list='$(SUBDIRS)'; for subdir in $$list; do \
+   cd $$subdir; \
+-  $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" 
CFLAGS="$(CFLAGS)" \
++  $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" 
CFLAGS="$(CFLAGS)" \
+   INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" 
$$target || exit 1; \
+   cd $$wdir; \
+   done;
+@@ -31,7 +31,7 @@
+   $(AR) -csru $@