From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/amos/Manifest | 10 ++ sci-biology/amos/amos-3.1.0-r3.ebuild | 48 ++++++++ .../amos/files/amos-3.1.0-fix-build-system.patch | 116 ++++++++++++++++++ sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 +++ ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ++++ sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch | 136 +++++++++++++++++++++ sci-biology/amos/metadata.xml | 11 ++ 7 files changed, 361 insertions(+) create mode 100644 sci-biology/amos/Manifest create mode 100644 sci-biology/amos/amos-3.1.0-r3.ebuild create mode 100644 sci-biology/amos/files/amos-3.1.0-fix-build-system.patch create mode 100644 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch create mode 100644 sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch create mode 100644 sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch create mode 100644 sci-biology/amos/metadata.xml (limited to 'sci-biology/amos') 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 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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 + #include + #include ++#include + 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::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 Maximum error rate for overlaps is \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 Set minimum overlap length to \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 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 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 ++#include ++ + 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 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + amos + + -- cgit v1.2.3