reinit the tree, so we can have metadata

7 files changed, 361 insertions, 0 deletions

diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
new file mode 100644
index 000000000000..5f8f3526e54d
--- /dev/null
+++ b/sci-biology/amos/Manifest
@@ -0,0 +1,10 @@
+AUX amos-3.1.0-fix-build-system.patch 3132 SHA256 1a78682189bcca5b7f896f8c88b63c45cded64dc90210f18ac6be73c39b19ba2 SHA512 b23c168c166f8a1dad89d1b25536a59be3e68a6478cef3db5664dc901cef0547213a8622a72ee1a2e1d5b8930c65d95e309573f903423e8fb80fb7312d89f863 WHIRLPOOL ab6aeb185c2eda629b168df776a9ddfcac611c2458627019459fa2fbdb5dcc393d8751a6e34e319bfe9db092c3df5892b355e18d598ac5f9e133968312d92922
+AUX amos-3.1.0-gcc-4.7.patch 400 SHA256 59be7e1fa3c4125f463e666f304f2194fc73026c71005ac16891e950e75b8af6 SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835 WHIRLPOOL 5c446c940eed42a5d8b47c102e97a4fc3c9818aa40f6049ab6b4e78ee8cf445665afbc78b9c2742e3de3adccb087e8f61ba3ebe567140d2e26d2a6167fe13b65
+AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 SHA256 6dba8f9c13ebabb5aa55c8b6ec71a015315662d00ee749df96e6715b9de45736 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f WHIRLPOOL 3abec572fa4384f7b4d60aa6cb5d3da945e9e78ab462757945e55f7a64440023a229a08ab40b861d9823d7694e5f92683459381865757f9ef284c228ac3409a2
+AUX amos-3.1.0-qa-Wformat.patch 4511 SHA256 afa52695df2d2493089386714acad8d420bcaf64ee0b47273440dac93c43731e SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe WHIRLPOOL 6e9de1a7a01b1cdb4c763205df9544d9653cb309675fa6ad250b033a99c70de24d0f0c1490222e3c18cd07f86cfa4b1946dbf64aab837e54efb61201dc53a5f8
+DIST amos-3.1.0-fix-c++14.patch.bz2 8033 SHA256 23b853959147466e7d766b1fe54e0afabfe3a89b84c89f788f2b8e749344efd6 SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 WHIRLPOOL d4530a5b3ff2a90419a1368a0e652bad367d2fb7601765ca42e8110ade87e8360f90070c0021aa25f5a6421815794a83491581e16fa9cb26be23bcb187840ff3
+DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61
+EBUILD amos-3.1.0-r3.ebuild 1089 SHA256 f5fd59da7b6523c22ea79bb235cb88a66899ac20cd58543e6442ab1dc9bfa8fd SHA512 5eaebe166daa11142d77e0d1623a46a0736a1d1180c6bc80ad246f67c684ad38ceba0cf179ea2a7af83c8c2785f24ed12f54c2a71d6a10fe7174f852e649ded8 WHIRLPOOL 25735963c50ebfa80aae91aa21e7effd9ddc67cea56aae9ba0558ff13f555318fdead0e93a796538016acc62fe748fa242fa476ed2d724fc618debce3e571de1
+MISC ChangeLog 2862 SHA256 f41c2ee7fe2ab280c70a7ab4dcfc7996fbaf88168da479b87cd4bb9286a0b68d SHA512 aba67e201ae372c89a3575f1173c9a0145826cba6f421ed6810cd97335ccc375e52e2b146bac6861ea9d061832bd6a7ee1904d4b2bdb3a920cb3ad83e04b20f0 WHIRLPOOL 152c685210d814b0133f14b00627dca6cb88f935429980e1775cda333436182cd09dc5579329b32108b63a68a787f595200457a406ca81617d763aed8f01a69c
+MISC ChangeLog-2015 2903 SHA256 acc84b2bce3b80f1badfbd7f077aa6ce126153381202ee7216fc690d71e6ded8 SHA512 4aed01fa4327bf98f4953d3c4007c4b2d2cf97d269f94733233134c21785ba356f915fe907019f862869e79edee801e3d4f4daac0f59feb18cab5e05c87870a0 WHIRLPOOL c7a8ac94dd18417292579f2a4b482877ce64050b2a263a8f0f30db94f36f800949216871e4726773335679c36df3581b189390b4d1280550490001f39343fe0e
+MISC metadata.xml 345 SHA256 d071906d7402159bb5834de6e489c5677a5e459e37aa05d0049f83d9e2784c81 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497 WHIRLPOOL 1610108ad99b2b6340c4c7cbf42f5230e0b08513a9efa7bda8030105025e19499c959e1c17ff8ae8aa2bce4f0234ad2b038bfd9840212080ce2edec5a6411a8e
diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild
new file mode 100644
index 000000000000..ab383a3b95a0
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r3.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools flag-o-matic python-single-r1
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt4"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+	${PYTHON_DEPS}
+	dev-perl/DBI
+	dev-perl/Statistics-Descriptive
+	sci-biology/mummer"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+	"${WORKDIR}"/${P}-fix-c++14.patch
+	"${FILESDIR}"/${P}-qa-Wformat.patch
+	"${FILESDIR}"/${P}-fix-build-system.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+
+	# prevent GCC 6 log pollution due
+	# to hash_map deprecation in C++11
+	append-cxxflags -Wno-cpp
+}
+
+src_install() {
+	default
+	python_fix_shebang "${ED%/}"/usr/bin/goBambus2
+}
diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
new file mode 100644
index 000000000000..9c824dd2f122
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
@@ -0,0 +1,116 @@
+* Use proper AR and not just 'ar'
+* Fix build system to build in parallel
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -34,6 +34,7 @@
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_RANLIB
++AM_PROG_AR
+ AC_PROG_CPP
+ AC_PATH_PROG(PERL, [perl], [:])
+ AC_PATH_PROG(PYTHON, [python], [:])
+--- a/src/Align/Makefile.am
++++ b/src/Align/Makefile.am
+@@ -133,7 +133,7 @@
+ 
+ ##-- hash-overlap
+ hash_overlap_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -172,7 +172,7 @@
+ 
+ ##-- make-consensus
+ make_consensus_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -182,7 +182,7 @@
+ 
+ ##-- make-consensus_poly
+ make_consensus_poly_LDADD = \
+-	$(top_builddir)/src/Align/libAlign_poly.a \
++	libAlign_poly.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -192,7 +192,7 @@
+ 
+ ##-- maligntest
+ maligntest_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -202,7 +202,7 @@
+ 
+ ##-- merge-contigs
+ merge_contigs_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -235,7 +235,7 @@
+ 
+ ##-- show-ma-asm
+ show_ma_asm_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+ 	$(top_builddir)/src/AMOS/libAMOS.a
+ show_ma_asm_SOURCES = \
+@@ -261,7 +261,7 @@
+ 
+ ##-- simple-overlap
+ simple_overlap_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+@@ -272,7 +272,7 @@
+ 
+ ##-- test-align
+ test_align_LDADD = \
+-	$(top_builddir)/src/Align/libAlign.a \
++	libAlign.a \
+ 	$(top_builddir)/src/CelMsg/libCelMsg.a \
+ 	$(top_builddir)/src/Slice/libSlice.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+--- a/src/Bambus/Bundler/Makefile.am
++++ b/src/Bambus/Bundler/Makefile.am
+@@ -47,7 +47,7 @@
+ 	clk.cc
+ 
+ MarkRepeats_LDADD = \
+-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
++	libBundler.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+ 	$(top_builddir)/src/AMOS/libAMOS.a \
+ 	$(top_builddir)/src/GNU/libGNU.a
+@@ -55,7 +55,7 @@
+ 	MarkRepeats.cc
+ 
+ OrientContigs_LDADD = \
+-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
++	libBundler.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+ 	$(top_builddir)/src/AMOS/libAMOS.a \
+ 	$(top_builddir)/src/GNU/libGNU.a
+@@ -63,7 +63,7 @@
+ 	OrientContigs.cc
+ 
+ FilterEdgesByCluster_LDADD = \
+-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
++	libBundler.a \
+ 	$(top_builddir)/src/Common/libCommon.a \
+ 	$(top_builddir)/src/AMOS/libAMOS.a \
+ 	$(top_builddir)/src/GNU/libGNU.a
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
new file mode 100644
index 000000000000..de2a41184c52
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/Align/find-tandem.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
+index ddf1cab..a29e21e 100644
+--- a/src/Align/find-tandem.cc
++++ b/src/Align/find-tandem.cc
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <ctime>
+ #include <sys/time.h>
++#include <unistd.h>
+ using namespace std;
+ 
+ const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
new file mode 100644
index 000000000000..97a8f59d0208
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
@@ -0,0 +1,25 @@
+--- amos-3.1.0/src/Pipeline/goBambus2.py.orig	2013-09-11 01:05:29.850090457 +0200
++++ amos-3.1.0/src/Pipeline/goBambus2.py	2013-09-11 01:07:03.250090701 +0200
+@@ -1,7 +1,7 @@
+ #pipeline script for assembly + Bambus 2
+ #contributed by Todd J Treangen
+ 
+-import string, sys, os, subprocess#, spincursor
++import sys, os, subprocess#, spincursor
+ 
+ RED =    "\033[0;31m"
+ GREEN =  "\033[0;32m"
+@@ -360,7 +360,7 @@
+                 print "\t\t%s...failed%s"%(RED,NONE)
+                 sys.exit(1)
+ 
+-       p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
++        p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
+ 
+         if xopt_dict["verbose"] == 1:
+             print "10) running OutputResults"
+@@ -388,4 +388,3 @@
+             else:
+                 print "\t\t%s...failed%s"%(RED,NONE)
+                 sys.exit(1)
+-)
diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
new file mode 100644
index 000000000000..13f4eeb247a1
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
@@ -0,0 +1,136 @@
+Fix QA warnings, due to using incorrect format specifiers in printf:
+* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’,
+* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=]
+*     fprintf (stderr, "%u b contigs\n", b . size ());
+
+--- a/src/Align/align.cc
++++ b/src/Align/align.cc
+@@ -1936,7 +1936,7 @@
+    n = align . size ();
+    con = consensus . c_str ();
+ 
+-   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
++   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
+ 
+    for  (i = 0;  i < n;  i ++)
+      {
+@@ -3936,7 +3936,7 @@
+         }
+ 
+       // Array of sum of quality scores in the slice for A,C,G,T,- resp.
+-      for (j = 0; j < 6; j ++)
++      for (j = 0; j < 5; j ++)
+         qvsum [j] = 0;
+ 
+       int nof_ambiguities = 0;
+--- a/src/Align/align_poly.cc
++++ b/src/Align/align_poly.cc
+@@ -1761,7 +1761,7 @@
+    n = align . size ();
+    con = consensus . c_str ();
+ 
+-   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
++   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
+    for  (i = 0;  i < n;  i ++)
+      {
+       fprintf (fp, "\nString #%d:\n", i);
+--- a/src/Align/count-qmers.cc
++++ b/src/Align/count-qmers.cc
+@@ -191,8 +191,8 @@
+ 
+     PrintMers(mer_table, min_count);
+ 
+-    fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT);
+-    fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n",    LEN);
++    fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT);
++    fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n",    LEN);
+   }
+   catch (Exception_t & e)
+   {
+--- a/src/Align/kmer-cov.cc
++++ b/src/Align/kmer-cov.cc
+@@ -485,7 +485,7 @@
+           Kmer_Len = s . length ();
+       else if  (Kmer_Len != int (s . length ()))
+           {
+-           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
++           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
+                 s . c_str (), s . length (), Kmer_Len);
+            Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
+           }
+--- a/src/Align/kmer-cov-plot.cc
++++ b/src/Align/kmer-cov-plot.cc
+@@ -316,7 +316,7 @@
+     }
+     else if  (Kmer_Len != int (s . length ()))
+     {
+-      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
++      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
+                s . c_str (), s . length (), Kmer_Len);
+       Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
+     }
+--- a/src/Align/make-consensus.cc
++++ b/src/Align/make-consensus.cc
+@@ -303,7 +303,7 @@
+             break;
+         }
+ 
+-        sprintf (sid, "%ld", ++layout_id);
++        sprintf (sid, "%u", ++layout_id);
+         cid = string (sid);
+         ID_t lid = layout.getIID ();
+         if (lid == 0)
+--- a/src/Align/make-consensus_poly.cc
++++ b/src/Align/make-consensus_poly.cc
+@@ -279,7 +279,7 @@
+ 		   break;
+ 	       }
+ 		 
+-	       sprintf(sid, "%ld", ++layout_id);
++	       sprintf(sid, "%u", ++layout_id);
+ 	       cid = string(sid);
+ 	       ID_t lid = layout.getIID();
+ 	       if (lid == 0) {
+--- a/src/Align/simple-overlap.cc
++++ b/src/Align/simple-overlap.cc
+@@ -422,7 +422,7 @@
+            "Options:\n"
+            "  -a       Also show alignments of overlaps \n"
+            "  -E <x>   Maximum error rate for overlaps is <x>\n"
+-           "           e.g., -E 0.06 for 6% error rate\n"
++           "           e.g., -E 0.06 for 6%% error rate\n"
+            "  -F       Input is a fasta file\n"
+            "  -h       Print this usage message\n"
+            "  -o <n>   Set minimum overlap length to <n>\n"
+--- a/src/Compare/contig-cmp.cc
++++ b/src/Compare/contig-cmp.cc
+@@ -145,7 +145,7 @@
+ 
+    fclose (fp);
+ 
+-   fprintf (stderr, "%u a contigs\n", a . size ());
++   fprintf (stderr, "%zu a contigs\n", a . size ());
+    vector <Unitig_t>  a_contig (max_id + 1);
+    n = a . size ();
+    for  (i = 0;  i < n;  i ++)
+@@ -234,7 +234,7 @@
+ 
+    fclose (fp);
+ 
+-   fprintf (stderr, "%u b contigs\n", b . size ());
++   fprintf (stderr, "%zu b contigs\n", b . size ());
+    vector <Unitig_t>  b_contig (max_id + 1);
+    n = b . size ();
+    for  (i = 0;  i < n;  i ++)
+--- a/src/Staden/progs/trace_convert.c
++++ b/src/Staden/progs/trace_convert.c
+@@ -6,6 +6,9 @@
+ #include "traceType.h"
+ #include "seqIOABI.h"
+ 
++#include <fcntl.h>
++#include <unistd.h>
++
+ static char fileIdentifier[] = "$Id$";
+ 
+ struct opts {
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
new file mode 100644
index 000000000000..2668bce2ac8a
--- /dev/null
+++ b/sci-biology/amos/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">amos</remote-id>
+  </upstream>
+</pkgmetadata>