diff options
Diffstat (limited to 'sci-biology/amos/files')
4 files changed, 292 insertions, 0 deletions
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 { |