From 671c4b6fa357bd05ffafc2f3215218067f1f1fed Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Sun, 14 Oct 2007 00:03:28 +0000 Subject: Adding various packages so I can work on them later... svn path=/; revision=87 --- sci-biology/meme/ChangeLog | 14 ++ sci-biology/meme/Manifest | 28 +++ sci-biology/meme/files/digest-meme-3.5.4 | 3 + sci-biology/meme/files/digest-meme-3.5.4-r1 | 3 + .../meme/files/meme-3.5.4-Makefile.am.patch | 17 ++ sci-biology/meme/files/meme-3.5.4-patch1.patch | 210 +++++++++++++++++++++ sci-biology/meme/files/meme-3.5.4-patch2.patch | 78 ++++++++ sci-biology/meme/files/meme_3.5.4.patch_1 | 198 +++++++++++++++++++ sci-biology/meme/files/meme_3.5.4.patch_2 | 70 +++++++ sci-biology/meme/meme-3.5.4.ebuild | 89 +++++++++ sci-biology/meme/metadata.xml | 5 + 11 files changed, 715 insertions(+) create mode 100644 sci-biology/meme/ChangeLog create mode 100644 sci-biology/meme/Manifest create mode 100644 sci-biology/meme/files/digest-meme-3.5.4 create mode 100644 sci-biology/meme/files/digest-meme-3.5.4-r1 create mode 100644 sci-biology/meme/files/meme-3.5.4-Makefile.am.patch create mode 100644 sci-biology/meme/files/meme-3.5.4-patch1.patch create mode 100644 sci-biology/meme/files/meme-3.5.4-patch2.patch create mode 100644 sci-biology/meme/files/meme_3.5.4.patch_1 create mode 100644 sci-biology/meme/files/meme_3.5.4.patch_2 create mode 100644 sci-biology/meme/meme-3.5.4.ebuild create mode 100644 sci-biology/meme/metadata.xml (limited to 'sci-biology/meme') diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog new file mode 100644 index 0000000..2275338 --- /dev/null +++ b/sci-biology/meme/ChangeLog @@ -0,0 +1,14 @@ +# ChangeLog for sci-biology/meme +# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.2 2007/09/17 02:41:56 je_fro Exp $ + + 17 Sep 2007; +files/meme-3.5.4-patch1.patch, + +files/meme-3.5.4-patch2.patch, meme-3.5.4.ebuild: + Remove parallel install for amd64 boxes, and add upstream patches. + +*meme-3.5.4 (24 Apr 2007) + + 24 Apr 2007; Olivier Fisette + +files/meme-3.5.4-Makefile.am.patch, +metadata.xml, +meme-3.5.4.ebuild: + Initial import. + diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest new file mode 100644 index 0000000..42e9a66 --- /dev/null +++ b/sci-biology/meme/Manifest @@ -0,0 +1,28 @@ +AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 +MD5 1340a30b4b010637181605a11e78a950 files/meme-3.5.4-Makefile.am.patch 377 +RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad files/meme-3.5.4-Makefile.am.patch 377 +SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 files/meme-3.5.4-Makefile.am.patch 377 +AUX meme-3.5.4-patch1.patch 8019 RMD160 c443da2f16552c488b77e897bdae543839a0738d SHA1 d37473061f4294d342521570729d65421ead0d99 SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6 +MD5 491211c1a3d87abd057280406f95220c files/meme-3.5.4-patch1.patch 8019 +RMD160 c443da2f16552c488b77e897bdae543839a0738d files/meme-3.5.4-patch1.patch 8019 +SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6 files/meme-3.5.4-patch1.patch 8019 +AUX meme-3.5.4-patch2.patch 2496 RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 SHA1 cbc691788e2d30cde438f15d94a97f637fdce4a5 SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21 +MD5 7b0765e479af87218368f29ae7041fb8 files/meme-3.5.4-patch2.patch 2496 +RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 files/meme-3.5.4-patch2.patch 2496 +SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21 files/meme-3.5.4-patch2.patch 2496 +DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 +EBUILD meme-3.5.4.ebuild 2778 RMD160 db6f29dd51ecf5bac56f064c75d788b36f56a83a SHA1 cebab3898c38b9396b2cf591f8ac49ff6ddc106b SHA256 05bd30158cc5b79c2de4f2e97c523f9cff48131965c992f24137bb2e36e006e0 +MD5 c71dbb29f70e8dfa3bc3ab607c33f226 meme-3.5.4.ebuild 2778 +RMD160 db6f29dd51ecf5bac56f064c75d788b36f56a83a meme-3.5.4.ebuild 2778 +SHA256 05bd30158cc5b79c2de4f2e97c523f9cff48131965c992f24137bb2e36e006e0 meme-3.5.4.ebuild 2778 +MISC ChangeLog 566 RMD160 74f3916e717ce84e593217bd53c0b99eb10a14c9 SHA1 799df7e3146993c26d897dd8224f302fd0970fcc SHA256 909bde96179b1488d0bcd854d9cd2d3a37a6e55c6c9756623fae0e77e8562dff +MD5 233146864b46de91b59ff4a506da21d7 ChangeLog 566 +RMD160 74f3916e717ce84e593217bd53c0b99eb10a14c9 ChangeLog 566 +SHA256 909bde96179b1488d0bcd854d9cd2d3a37a6e55c6c9756623fae0e77e8562dff ChangeLog 566 +MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 +MD5 aec0225cc3c4bc9490275e897849b449 metadata.xml 165 +RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 metadata.xml 165 +SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 metadata.xml 165 +MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4 235 +RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4 235 +SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4 235 diff --git a/sci-biology/meme/files/digest-meme-3.5.4 b/sci-biology/meme/files/digest-meme-3.5.4 new file mode 100644 index 0000000..01fad30 --- /dev/null +++ b/sci-biology/meme/files/digest-meme-3.5.4 @@ -0,0 +1,3 @@ +MD5 9a8b3d21c6094616cc7b9b424352c697 meme_3.5.4.tar.gz 1045501 +RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 meme_3.5.4.tar.gz 1045501 +SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 meme_3.5.4.tar.gz 1045501 diff --git a/sci-biology/meme/files/digest-meme-3.5.4-r1 b/sci-biology/meme/files/digest-meme-3.5.4-r1 new file mode 100644 index 0000000..01fad30 --- /dev/null +++ b/sci-biology/meme/files/digest-meme-3.5.4-r1 @@ -0,0 +1,3 @@ +MD5 9a8b3d21c6094616cc7b9b424352c697 meme_3.5.4.tar.gz 1045501 +RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 meme_3.5.4.tar.gz 1045501 +SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 meme_3.5.4.tar.gz 1045501 diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch new file mode 100644 index 0000000..1293de0 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch @@ -0,0 +1,17 @@ +--- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400 ++++ Makefile.am 2007-04-24 10:37:37.000000000 -0400 +@@ -57,11 +57,11 @@ + endif + + dbdir: +- mkdir -p $(MEME_DB) ++ mkdir -p $(DESTDIR)$(MEME_DB) + + install-data-local: +- mkdir -p $(MEME_LOGS) +- chmod a+w $(MEME_LOGS) ++ mkdir -p $(DESTDIR)$(MEME_LOGS) ++ chmod a+w $(DESTDIR)$(MEME_LOGS) + + distdir = $(PACKAGE)_$(VERSION) + diff --git a/sci-biology/meme/files/meme-3.5.4-patch1.patch b/sci-biology/meme/files/meme-3.5.4-patch1.patch new file mode 100644 index 0000000..09a9498 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch1.patch @@ -0,0 +1,210 @@ +--- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ ++## $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + ## + ## $Log: meme-3.5.4-patch1.patch,v $ + ## Revision 1.1 2007/09/17 02:41:56 je_fro + ## Add upstream patches and disable parallel install on amd64. + ## (Portage version: 2.1.3.9) + ## + ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya +@@ -55,7 +55,8 @@ + $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl"; + # + # You can change this if you wish to use a different JASPAR server +-$jaspar_root = "http://mordor.cgb.ki.se"; ++#$jaspar_root = "http://mordor.cgb.ki.se"; ++$jaspar_root = "http://asp.ii.uib.no:8090"; + $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl"; + # + # You can change this if you wish to use a different Meta-MEME server +@@ -221,7 +222,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get sequence line +@@ -239,7 +240,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get id line and sequence line +@@ -311,7 +312,8 @@ + $content = $request->content; + + # fix bug in JASPAR output; add database field to view buttons +- $content =~ s/rm=present/rm=present&db=$sub_db/g; ++ # remove fix: JASPAR fixed the bug ++ # $content =~ s/rm=present/rm=present&db=$sub_db/g; + + # display the page + print $content; +--- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ ++ * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + * + * $Log: meme-3.5.4-patch1.patch,v $ + * Revision 1.1 2007/09/17 02:41:56 je_fro + * Add upstream patches and disable parallel install on amd64. + * (Portage version: 2.1.3.9) + * + * Revision 1.2 2006/03/08 20:50:11 nadya +@@ -206,10 +206,9 @@ + + Local void addinfo(char *s, struct ReadSeqVars *V) + { +- char s2[256], *si; ++ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char)); + boolean saveadd; + +- si = s2; + while (*s == ' ') s++; + sprintf(si, " %d) %s\n", V->nseq, s); + +@@ -217,6 +216,7 @@ + V->addit = true; + V->isseqchar = isAnyChar; + addseq( si, V); ++ free(si); + V->addit = saveadd; + V->isseqchar = isSeqChar; + } +@@ -966,7 +966,6 @@ + } while ((l == 0) && !feof(V->f)); + + if (feof(V->f)) V->err = eNoData; +- + else switch (format_) { + case kPlain : readPlain(V); break; + case kIG : readIG(V); break; +@@ -1181,7 +1180,7 @@ + int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0; + char sp[MAXLINE]; + long linestart=0; +- int maxlines2check=500; ++ int maxlines2check=5000; + + #define ReadOneLine(sp) \ + { done |= (feof(fseq)); \ +--- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ ++ * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + * + * $Log: meme-3.5.4-patch1.patch,v $ + * Revision 1.1 2007/09/17 02:41:56 je_fro + * Add upstream patches and disable parallel install on amd64. + * (Portage version: 2.1.3.9) + * + * Revision 1.1 2005/07/29 19:12:07 nadya +@@ -15,7 +15,7 @@ + #include "config.h" + #include "macros.h" + +-#define MAXLINE 1024 ++#define MAXLINE 10240 + + typedef char boolean; + #define NEWLINE '\n' +--- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000 ++++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000 +@@ -433,6 +433,7 @@ + name[i++] = c; /* non-blank: add to name */ + } + } ++ Resize(name, i+1, char); + name[i] = '\0'; + + /* read in description */ +--- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000 ++++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000 +@@ -208,42 +208,39 @@ +

Getting and installing the patches

+

The distribution may have patches associated with it. They are available + from http://meme.nbcr.net/downloads/. +-The patch file name is filename.VERSION.patch. In addition, a +-patched file is distributed as well and can be used as a drop-in substitute +-for the original file. The drop-in file is filename.VERSION. +-It is necessary to download only one of the two files depending on the method used for +-patching. All patches for a specific version should be installed. The list +-below provides instructions for installation of availble patches for specific +-version. ++Patch files are located in a directory named ++VERSION.patches, ++for example, meme_3.5.4.patches. ++Patch file have names like: ++VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3. ++

To install a patch, download the patch file from the URL given above. ++Then perform the following commands to install it: ++
$ cp PATCH_FILE VERSION
$ cd VERSION ++
$ patch -p1 < PATCH_FILE ++
$ make install ++
$ make test ++

++

++For example, to install the first patch to version meme_3.5.4, you would perform the following commands: ++
$ cp meme_3.5.4.patch_1 meme_3.5.4 ++
$ cd meme_3.5.4 ++
$ patch -p1 < meme_3.5.4.patch_1 ++
$ make install ++
$ make test ++

++

++You must install all of the patches for a specific version in serial ++number order. For example, if you wish to install patch number 3, ++you must first have installed patches number 1 and 2 for that version. ++This is easy to do. Just download all the patches for your current ++version, copy them to your current versions's directory, and then ++install them in order by repeating the patch, ++command above, with each patch file. You only need to run the ++install and ++make test commands once, after ++the last patch command. +

+ +-
+- +- +- +- +- +- +- +- +- +- +- +-
VersionPatch listInstallation
3.5.0mast-client.txt +-
    +-
  1. If downloaded a patch file mast-client.txt.3.5.0.patch: +-
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/ +-
    # cd meme_3.5.0/scripts/ +-
    # patch -p0 < mast-client.txt.3.5.0.patch +-
    +-
    2. +-
  2. If downloaded a patched file mast-client.txt.3.5.0: +-
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt +-
    3. +-
+-
+-
+- +

+

[ Top ]

+ diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch new file mode 100644 index 0000000..3854b83 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch @@ -0,0 +1,78 @@ +--- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ ++## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + ## + ## $Log: meme-3.5.4-patch2.patch,v $ + ## Revision 1.1 2007/09/17 02:41:56 je_fro + ## Add upstream patches and disable parallel install on amd64. + ## (Portage version: 2.1.3.9) + ## + ## Revision 1.12 2006/03/07 23:30:19 nadya +@@ -467,21 +467,21 @@ + + # check against allowed dna letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + "dna"; + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + "protein"; + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. +
+--- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ ++## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + ## + ## $Log: meme-3.5.4-patch2.patch,v $ + ## Revision 1.1 2007/09/17 02:41:56 je_fro + ## Add upstream patches and disable parallel install on amd64. + ## (Portage version: 2.1.3.9) + ## + ## Revision 1.8 2006/03/07 23:30:19 nadya +@@ -479,21 +479,21 @@ + + # check against allowed nucleotide letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + return("DNA"); + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + return("PROTEIN"); + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. +
diff --git a/sci-biology/meme/files/meme_3.5.4.patch_1 b/sci-biology/meme/files/meme_3.5.4.patch_1 new file mode 100644 index 0000000..b072d7e --- /dev/null +++ b/sci-biology/meme/files/meme_3.5.4.patch_1 @@ -0,0 +1,198 @@ +--- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $ + ## + ## $Log: process_request.pl,v $ + ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya +@@ -55,7 +55,8 @@ + $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl"; + # + # You can change this if you wish to use a different JASPAR server +-$jaspar_root = "http://mordor.cgb.ki.se"; ++#$jaspar_root = "http://mordor.cgb.ki.se"; ++$jaspar_root = "http://asp.ii.uib.no:8090"; + $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl"; + # + # You can change this if you wish to use a different Meta-MEME server +@@ -221,7 +222,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get sequence line +@@ -239,7 +240,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get id line and sequence line +@@ -311,7 +312,8 @@ + $content = $request->content; + + # fix bug in JASPAR output; add database field to view buttons +- $content =~ s/rm=present/rm=present&db=$sub_db/g; ++ # remove fix: JASPAR fixed the bug ++ # $content =~ s/rm=present/rm=present&db=$sub_db/g; + + # display the page + print $content; +--- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $ ++ * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $ + * + * $Log$ + * Revision 1.2 2006/03/08 20:50:11 nadya +@@ -206,10 +206,9 @@ + + Local void addinfo(char *s, struct ReadSeqVars *V) + { +- char s2[256], *si; ++ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char)); + boolean saveadd; + +- si = s2; + while (*s == ' ') s++; + sprintf(si, " %d) %s\n", V->nseq, s); + +@@ -217,6 +216,7 @@ + V->addit = true; + V->isseqchar = isAnyChar; + addseq( si, V); ++ free(si); + V->addit = saveadd; + V->isseqchar = isSeqChar; + } +@@ -966,7 +966,6 @@ + } while ((l == 0) && !feof(V->f)); + + if (feof(V->f)) V->err = eNoData; +- + else switch (format_) { + case kPlain : readPlain(V); break; + case kIG : readIG(V); break; +@@ -1181,7 +1180,7 @@ + int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0; + char sp[MAXLINE]; + long linestart=0; +- int maxlines2check=500; ++ int maxlines2check=5000; + + #define ReadOneLine(sp) \ + { done |= (feof(fseq)); \ +--- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $ ++ * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $ + * + * $Log$ + * Revision 1.1 2005/07/29 19:12:07 nadya +@@ -15,7 +15,7 @@ + #include "config.h" + #include "macros.h" + +-#define MAXLINE 1024 ++#define MAXLINE 10240 + + typedef char boolean; + #define NEWLINE '\n' +--- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000 ++++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000 +@@ -433,6 +433,7 @@ + name[i++] = c; /* non-blank: add to name */ + } + } ++ Resize(name, i+1, char); + name[i] = '\0'; + + /* read in description */ +--- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000 ++++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000 +@@ -208,42 +208,39 @@ +

Getting and installing the patches

+

The distribution may have patches associated with it. They are available + from http://meme.nbcr.net/downloads/. +-The patch file name is filename.VERSION.patch. In addition, a +-patched file is distributed as well and can be used as a drop-in substitute +-for the original file. The drop-in file is filename.VERSION. +-It is necessary to download only one of the two files depending on the method used for +-patching. All patches for a specific version should be installed. The list +-below provides instructions for installation of availble patches for specific +-version. ++Patch files are located in a directory named ++VERSION.patches, ++for example, meme_3.5.4.patches. ++Patch file have names like: ++VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3. ++

To install a patch, download the patch file from the URL given above. ++Then perform the following commands to install it: ++
$ cp PATCH_FILE VERSION
$ cd VERSION ++
$ patch -p1 < PATCH_FILE ++
$ make install ++
$ make test ++

++

++For example, to install the first patch to version meme_3.5.4, you would perform the following commands: ++
$ cp meme_3.5.4.patch_1 meme_3.5.4 ++
$ cd meme_3.5.4 ++
$ patch -p1 < meme_3.5.4.patch_1 ++
$ make install ++
$ make test ++

++

++You must install all of the patches for a specific version in serial ++number order. For example, if you wish to install patch number 3, ++you must first have installed patches number 1 and 2 for that version. ++This is easy to do. Just download all the patches for your current ++version, copy them to your current versions's directory, and then ++install them in order by repeating the patch, ++command above, with each patch file. You only need to run the ++install and ++make test commands once, after ++the last patch command. +

+ +-
+- +- +- +- +- +- +- +- +- +- +- +-
VersionPatch listInstallation
3.5.0mast-client.txt +-
    +-
  1. If downloaded a patch file mast-client.txt.3.5.0.patch: +-
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/ +-
    # cd meme_3.5.0/scripts/ +-
    # patch -p0 < mast-client.txt.3.5.0.patch +-
    +-
    2. +-
  2. If downloaded a patched file mast-client.txt.3.5.0: +-
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt +-
    3. +-
+-
+-
+- +

+

[ Top ]

+ diff --git a/sci-biology/meme/files/meme_3.5.4.patch_2 b/sci-biology/meme/files/meme_3.5.4.patch_2 new file mode 100644 index 0000000..cc07a98 --- /dev/null +++ b/sci-biology/meme/files/meme_3.5.4.patch_2 @@ -0,0 +1,70 @@ +--- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $ + ## + ## $Log$ + ## Revision 1.12 2006/03/07 23:30:19 nadya +@@ -467,21 +467,21 @@ + + # check against allowed dna letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + "dna"; + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + "protein"; + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. +
+--- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $ + ## + ## $Log$ + ## Revision 1.8 2006/03/07 23:30:19 nadya +@@ -479,21 +479,21 @@ + + # check against allowed nucleotide letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + return("DNA"); + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + return("PROTEIN"); + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. +
diff --git a/sci-biology/meme/meme-3.5.4.ebuild b/sci-biology/meme/meme-3.5.4.ebuild new file mode 100644 index 0000000..1932bd7 --- /dev/null +++ b/sci-biology/meme/meme-3.5.4.ebuild @@ -0,0 +1,89 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.4-r1.ebuild,v 1.1 2007/09/17 02:41:56 je_fro Exp $ + +inherit eutils toolchain-funcs + +DESCRIPTION="The MEME/MAST system - Motif discovery and search" +HOMEPAGE="http://meme.sdsc.edu/meme" +SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz" +LICENSE="meme" + +SLOT="0" +KEYWORDS="~x86 ~amd64" +# Other possible USE flags include "debug", "client", "server", "web", +# "queue". Other variables must be set at compile time, but only when +# the Web server is built. Right now, Web server and client are disabled. +IUSE="mpi" + +# Works only with LAM-MPI. +DEPEND=">=dev-lang/perl-5.6.1 + mpi? ( sys-cluster/lam-mpi )" + +S="${WORKDIR}/${PN}_${PV}" + +src_unpack() { + unpack ${A} + + cd "${S}" + epatch "${FILESDIR}/${P}-Makefile.am.patch" + epatch "${FILESDIR}/${P}-patch1.patch" + epatch "${FILESDIR}/${P}-patch2.patch" + eautoreconf +} + +src_compile() { + local EXTRA_CONF + # Build system is too bugy to make the programs use standard locations. + # Put everything in "/opt" instead. + EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}" + EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}" + # Connect hyperlinks to official Web site. + EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme" + # Disable Web server, client and Web site. + EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web" + # Parallel implementation + if ! use mpi; then + EXTRA_CONF="${EXTRA_CONF} --enable-serial" + fi + + ./configure ${EXTRA_CONF} || die "Configure failed." + CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}" make -e || die "Make failed." + +# Install parallel files only on x86, otherwise the install fails with the error: +# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output + if [[ "${ARCH}" == "x86" ]] ; then + if use mpi; then + cd src/parallel + make || die "Parallel make failed." + fi + fi +} + +src_install() { + make install DESTDIR="${D}" || die "Failed to install program files." + exeinto "/opt/${PN}/bin" + if [[ "${ARCH}" == "x86" ]] ; then + if use mpi; then + doexe "${S}/src/parallel/${PN}_p" || \ + die "Failed to install parallel MEME implementation." + fi + fi + keepdir "/var/log/${PN}" + fperms 777 "/var/log/${PN}" +} + +pkg_postinst() { + echo + einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"' + einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do' + einfo 'this automatically with bash, add the following statement to your' + einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".' + echo + einfo 'Log files are produced in the "/var/log/meme" directory.' + echo +} + +src_test() { + make test || die "Regression tests failed." +} diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml new file mode 100644 index 0000000..d464821 --- /dev/null +++ b/sci-biology/meme/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology + -- cgit v1.2.3-65-gdbad