[med-svn] r12793 - in trunk/packages/meme/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Jan 15 11:00:22 UTC 2013
Author: tille
Date: 2013-01-15 11:00:22 +0000 (Tue, 15 Jan 2013)
New Revision: 12793
Added:
trunk/packages/meme/trunk/debian/meme.docs
trunk/packages/meme/trunk/debian/patches/10_do_not_create_log_dir.patch
trunk/packages/meme/trunk/debian/patches/patch_4.9.0_1
trunk/packages/meme/trunk/debian/patches/patch_4.9.0_2
trunk/packages/meme/trunk/debian/patches/readme_patchlevel.html
Modified:
trunk/packages/meme/trunk/debian/changelog
trunk/packages/meme/trunk/debian/patches/fix_plib_path
trunk/packages/meme/trunk/debian/patches/series
trunk/packages/meme/trunk/debian/rules
Log:
Find some weak way to incorporate patches - just to enable users testing the latest patchlevel of meme but not intended as a final solution for the packaging
Modified: trunk/packages/meme/trunk/debian/changelog
===================================================================
--- trunk/packages/meme/trunk/debian/changelog 2013-01-14 15:31:34 UTC (rev 12792)
+++ trunk/packages/meme/trunk/debian/changelog 2013-01-15 11:00:22 UTC (rev 12793)
@@ -1,4 +1,4 @@
-meme (4.9.0-1) UNRELEASED; urgency=low
+meme (4.9.0p2-1) UNRELEASED; urgency=low
[ Thorsten Alteholz ]
* Initial release (Closes: #xxxxxx)
@@ -12,5 +12,9 @@
- install patches from
ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/patches/readme.html
as quilt patches
+ Currently: Download patches in get-orig-source target and echo hint what to do
+ Questionable: placing readme_patchlevel.html debian/patches - but somehow it is
+ close to the patches so the danger to mix it up with just another quilt patch
+ is not that hard
- -- Andreas Tille <tille at debian.org> Mon, 14 Jan 2013 10:06:12 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 15 Jan 2013 11:49:13 +0100
Added: trunk/packages/meme/trunk/debian/meme.docs
===================================================================
--- trunk/packages/meme/trunk/debian/meme.docs (rev 0)
+++ trunk/packages/meme/trunk/debian/meme.docs 2013-01-15 11:00:22 UTC (rev 12793)
@@ -0,0 +1 @@
+debian/patches/readme_patchlevel.html
Added: trunk/packages/meme/trunk/debian/patches/10_do_not_create_log_dir.patch
===================================================================
--- trunk/packages/meme/trunk/debian/patches/10_do_not_create_log_dir.patch (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/10_do_not_create_log_dir.patch 2013-01-15 11:00:22 UTC (rev 12793)
@@ -0,0 +1,30 @@
+--- meme_4.5.0.orig/Makefile.am
++++ meme_4.5.0/Makefile.am
+@@ -11,9 +11,9 @@
+ dbdir:
+ mkdir -p $(MEME_DB)
+
+-install-data-local:
+- mkdir -p $(MEME_LOGS)
+- chmod a+w $(MEME_LOGS)
++#install-data-local:
++# mkdir -p $(MEME_LOGS)
++# chmod a+w $(MEME_LOGS)
+
+ distdir = $(PACKAGE)_$(VERSION)
+
+--- meme_4.5.0.orig/Makefile.in
++++ meme_4.5.0/Makefile.in
+@@ -763,9 +763,9 @@
+ dbdir:
+ mkdir -p $(MEME_DB)
+
+-install-data-local:
+- mkdir -p $(MEME_LOGS)
+- chmod a+w $(MEME_LOGS)
++#install-data-local:
++# mkdir -p $(MEME_LOGS)
++# chmod a+w $(MEME_LOGS)
+
+ distclean-local: clean-local
+ clean-local: clean-ac
Modified: trunk/packages/meme/trunk/debian/patches/fix_plib_path
===================================================================
--- trunk/packages/meme/trunk/debian/patches/fix_plib_path 2013-01-14 15:31:34 UTC (rev 12792)
+++ trunk/packages/meme/trunk/debian/patches/fix_plib_path 2013-01-15 11:00:22 UTC (rev 12793)
@@ -1,8 +1,12 @@
Description: move plib to the correct Debian directory
+Remark: It seems plib is not used any more and also breaks in connection
+ with patch_4.9.0_2, so this patch is deactivated
+LastChangedBy: Andreas Tille <tille at debian.org>
+LastChanged: Tue, 15 Jan 2013 11:49:13 +0100
--- a/src/init.c
+++ b/src/init.c
-@@ -33,8 +33,9 @@
+@@ -34,8 +34,9 @@
#endif
/* priors */
@@ -14,15 +18,3 @@
#define ROUNDERROR (1E-12)
-@@ -495,9 +496,11 @@ void init_meme(
- plib_name = DNA_PLIB; /* default mixture prior for DNA */
- }
- /* prepend meme_directory to file name */
-+ /*
- Strcat(tmp1, meme_directory, "/etc/");
- Strcat(tmp2, tmp1, plib_name);
- plib_name = tmp2;
-+ */
- }
- }
- if ((ptype == Mega || ptype == MegaP) && beta == -1) {
Added: trunk/packages/meme/trunk/debian/patches/patch_4.9.0_1
===================================================================
--- trunk/packages/meme/trunk/debian/patches/patch_4.9.0_1 (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/patch_4.9.0_1 2013-01-15 11:00:22 UTC (rev 12793)
@@ -0,0 +1,252 @@
+diff -r 02aa25f920a7 -r caa80f3ff934 etc/centrimo_template.html
+--- a/etc/centrimo_template.html Fri Oct 05 09:45:00 2012 +1000
++++ b/etc/centrimo_template.html Fri Oct 05 00:26:25 2012 -0700
+@@ -371,7 +371,7 @@
+ <label for="windo">Window:</label>
+ <input type="number" style="min-width:40px;" id="windo"
+ onkeypress="num_keys(event)"
+- onchange="recreate_table=true; make_MP_graph(); recreate_table=false" value="20" size="2" min="1">
++ onchange="recreate_table=true; make_MP_graph(); recreate_table=false" value="20" size="2" step="1" min="1">
+ </div>
+ <div>
+ <label for="legend">Legend:</label>
+@@ -507,7 +507,7 @@
+ onclick="toggle_filter(this, 'filter_top')">
+ <label for="filter_top"
+ onclick="enable_filter('filter_on_top', 'filter_top')">Top</label>
+- <input type="number" id="filter_top" value="10" size="4" min="1"
++ <input type="number" id="filter_top" value="10" size="4" min="1" step="1"
+ onkeypress="num_keys(event); update_filter(event)" disabled>
+ </div>
+ <div >
+diff -r 02aa25f920a7 -r caa80f3ff934 website/cgi-bin/centrimo.tmpl
+--- a/website/cgi-bin/centrimo.tmpl Fri Oct 05 09:45:00 2012 +1000
++++ b/website/cgi-bin/centrimo.tmpl Fri Oct 05 00:26:25 2012 -0700
+@@ -165,7 +165,7 @@
+ </p>
+ </div>
+ <div class="meme">
+- <form enctype="multipart/form-data" method="POST" action="centrimo.cgi"
++ <form enctype="multipart/form-data" method="POST" novalidate action="centrimo.cgi"
+ onsubmit="return on_form_submit()" onreset="return on_form_reset()">
+ <fieldset>
+ <legend>Data Submission Form</legend>
+@@ -301,7 +301,7 @@
+ <h3 class="meme">Set a minimum acceptable match score (bits)</h3>
+ <label for="min_score">score ≥</label>
+ <input class="meme" type="number" id="min_score"
+- name="min_score" size="3" value="5">
++ name="min_score" size="3" value="5" step="any">
+ <input class="meme" type="checkbox" id="opt_score"
+ name="opt_score" value="1" style="margin-left:20px;">
+ <label for="opt_score">optimize score?</label>
+@@ -314,14 +314,14 @@
+ <label for="max_region"
+ onclick="$('use_max_region').click()">region width ≤</label>
+ <input class="meme" type="number" id="max_region"
+- name="max_region" size="5" value="200"
++ name="max_region" size="5" value="200" step="0.5"
+ onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_max_region')"></div>
+
+ <h3 class="meme">Set <i>E</i>-value threshold for reporting enriched regions</h3>
+ <label for="ethresh"><i>E</i>-value ≤</label>
+ <input class="meme" type="number" id="ethresh"
+- name="ethresh" size="5" value="10">
++ name="ethresh" size="5" value="10" min="0" step="any">
+ <div class="help" onclick="help_popup(this, 'pop_evalue_threshold')"></div>
+
+ <h3 class="meme">Allow comparative sequences for binomial test?</h3>
+diff -r 02aa25f920a7 -r caa80f3ff934 website/cgi-bin/dreme.tmpl
+--- a/website/cgi-bin/dreme.tmpl Fri Oct 05 09:45:00 2012 +1000
++++ b/website/cgi-bin/dreme.tmpl Fri Oct 05 00:26:25 2012 -0700
+@@ -94,7 +94,7 @@
+ </p>
+ </div>
+ <div class="meme">
+- <form enctype="multipart/form-data" method="POST" action="dreme.cgi" onsubmit="return check()">
++ <form enctype="multipart/form-data" method="POST" action="dreme.cgi" novalidate onsubmit="return check()">
+ <fieldset>
+ <legend>Data Submission Form</legend>
+ <p class="meme">Discover short regular expression motifs.</p>
+@@ -194,7 +194,7 @@
+ ≤
+ <!-- without html 5 support this is just a text field -->
+ <input type="number" name="limit_evalue" id="limit_evalue"
+- class="meme" step="0.05" value="0.05" size="4">
++ class="meme" step="any" value="0.05" min="0" size="4">
+ <div class="help" onclick="help_popup(this, 'pop_limit_evalue')"></div><br/>
+ <!-- /maximum evalue -->
+ <!-- maximum count -->
+@@ -208,7 +208,7 @@
+ </span> ≤
+ <!-- without html 5 support this is just a text field -->
+ <input type="number" name="limit_count" id="limit_count"
+- class="meme" disabled="disabled" step="1" value="10" size="4">
++ class="meme" disabled="disabled" step="1" min="1" value="10" size="4">
+ <div class="help" onclick="help_popup(this, 'pop_limit_count')"></div><br/>
+ <!-- /maximum count -->
+ <p>Note that the DREME webservice also enforces a time limit
+diff -r 02aa25f920a7 -r caa80f3ff934 website/cgi-bin/meme-chip.pl
+--- a/website/cgi-bin/meme-chip.pl Fri Oct 05 09:45:00 2012 +1000
++++ b/website/cgi-bin/meme-chip.pl Fri Oct 05 00:26:25 2012 -0700
+@@ -177,7 +177,7 @@
+ $d{MEME_PAL} = $utils->param_bool($q, 'meme_pal');
+ # DREME Specific Options
+ # get the motif E-value cut-off threshold
+- $d{DREME_E} = $utils->param_num($q, 'dreme_ethresh', 0, undef, 0.05);
++ $d{DREME_E} = $utils->param_num($q, 'dreme_ethresh', 'DREME E-value threshold', 0, undef, 0.05);
+ # get the optional motif count cut-off
+ if ($utils->param_bool($q, 'dreme_nmotifs_enable')) {
+ $d{DREME_M} = $utils->param_int($q, 'dreme_nmotifs',
+@@ -185,13 +185,13 @@
+ }
+ # CentriMo Specific Options
+ # Get the minimum acceptable site score
+- $d{CENTRIMO_SCORE} = $utils->param_num($q, 'centrimo_score', undef, undef, 5);
++ $d{CENTRIMO_SCORE} = $utils->param_num($q, 'centrimo_score', 'CentriMo minimum match score', undef, undef, 5);
+ # Get the optional maximum central window
+ if ($utils->param_bool($q, 'centrimo_maxreg_enable')) {
+- $d{CENTRIMO_MAXREG} = $utils->param_int($q, 'centrimo_maxreg', 1, undef, 200);
++ $d{CENTRIMO_MAXREG} = $utils->param_num($q, 'centrimo_maxreg', 'CentriMo maximum central region width', 1, undef, 200);
+ }
+ # get the maximum central enrichment E-value to report
+- $d{CENTRIMO_ETHRESH} = $utils->param_num($q, 'centrimo_ethresh', 0, undef, 10);
++ $d{CENTRIMO_ETHRESH} = $utils->param_num($q, 'centrimo_ethresh', 'CentriMo E-value threshold', 0, undef, 10);
+ # get if the seq IDs should be stored
+ $d{CENTRIMO_STORE_IDS} = $utils->param_bool($q, 'centrimo_store_ids');
+
+diff -r 02aa25f920a7 -r caa80f3ff934 website/cgi-bin/meme-chip.tmpl
+--- a/website/cgi-bin/meme-chip.tmpl Fri Oct 05 09:45:00 2012 +1000
++++ b/website/cgi-bin/meme-chip.tmpl Fri Oct 05 00:26:25 2012 -0700
+@@ -213,7 +213,7 @@
+ </div>
+ <div class="meme">
+ <form enctype="multipart/form-data" accept-charset="utf-8"
+- method="POST" action="meme-chip.cgi"
++ method="POST" action="meme-chip.cgi" novalidate
+ onsubmit="return on_form_submit()" onreset="return on_form_reset()">
+ <fieldset>
+ <legend>Data Submission Form</legend>
+@@ -322,20 +322,23 @@
+
+ <h3 class="meme">How many motifs should MEME find?</h3>
+ <label for="meme_nmotifs">Count of motifs:</label>
+- <input class="meme" type="number" name="meme_nmotifs" value="3"
+- size="2" id="meme_nmotifs" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="meme_nmotifs" value="3"
++ step="1" min="1" size="2" id="meme_nmotifs"
++ onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_meme_nmotifs')"></div>
+
+ <h3 class="meme">What width motifs should MEME find?</h3>
+ <span style="display:inline-block; min-width:12em;">
+ <label for="meme_minw">Minimum width:</label>
+- <input class="meme" type="number" name="meme_minw" value="6"
+- size="2" id="meme_minw" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="meme_minw" value="6"
++ step="1" min="2" max="300" size="2" id="meme_minw"
++ onkeypress="num_key(event)">
+ </span>
+
+ <label for="meme_maxw">Maximum width:</label>
+- <input class="meme" type="number" name="meme_maxw" value="30"
+- size="2" id="meme_maxw" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="meme_maxw" value="30"
++ step="1" min="2" max="300" size="2" id="meme_maxw"
++ onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_meme_width')"></div>
+
+ <div id="meme_sites">
+@@ -346,16 +349,18 @@
+ onclick="$('meme_minsites').disabled = !this.checked">
+ <label for="meme_minsites"
+ onclick="$('meme_minsites_enable').click()">Minimum sites:</label>
+- <input class="meme" type="number" name="meme_minsites" value="2"
+- size="2" id="meme_minsites" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="meme_minsites"
++ value="2" step="1" min="2" max="600" size="2"
++ id="meme_minsites" onkeypress="num_key(event)">
+ </span>
+ <input type="checkbox" value="1"
+ name="meme_maxsites_enable" id="meme_maxsites_enable"
+ onclick="$('meme_maxsites').disabled = !this.checked">
+ <label for="meme_maxsites"
+ onclick="$('meme_maxsites_enable').click()">Maximum sites:</label>
+- <input class="meme" type="number" name="meme_maxsites" value="600"
+- size="3" id="meme_maxsites" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="meme_maxsites"
++ value="600" step="1" min="2" max="600" size="3"
++ id="meme_maxsites" onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_meme_sites')"></div>
+ </div>
+
+@@ -382,15 +387,17 @@
+ <span style="display:inline-block; min-width:12em;">
+ <label for="dreme_ethresh"><i>E</i>-value ≤</label>
+ <input class="meme" type="number" name="dreme_ethresh"
+- id="dreme_ethresh" value="0.05" size="3">
++ value="0.05" step="any" min="0" size="3"
++ id="dreme_ethresh">
+ </span>
+ <input class="meme" type="checkbox" name="dreme_nmotifs_enable"
+ value="1" id="dreme_nmotifs_enable"
+ onclick="$('dreme_nmotifs').disabled = !this.checked">
+ <label for="dreme_nmotifs"
+ onclick="$('dreme_nmotifs_enable').click()">Count ≤</label>
+- <input class="meme" type="number" name="dreme_nmotifs" value="10"
+- size="2" id="dreme_nmotifs" onkeypress="num_key(event)">
++ <input class="meme" type="number" name="dreme_nmotifs"
++ value="10" step="1" min="1" size="2"
++ id="dreme_nmotifs" onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_dreme_limits')"></div>
+ </div>
+ <!-- /DREME Options -->
+@@ -410,7 +417,7 @@
+ <h3 class="meme">Set a minimum acceptable match score (bits)</h3>
+ <label for="centrimo_score">score ≥</label>
+ <input class="meme" type="number" name="centrimo_score"
+- size="3" value="5" id="centrimo_score">
++ size="3" value="5" step="any" id="centrimo_score">
+ <div class="help" onclick="help_popup(this, 'pop_centrimo_score')"></div>
+
+ <h3 class="meme">Set the maximum allowed width of central region</h3>
+@@ -421,13 +428,15 @@
+ onclick="$('centrimo_maxreg_enable').click()"
+ >region width ≤</label>
+ <input class="meme" type="number" name="centrimo_maxreg"
+- size="5" value="200" id="centrimo_maxreg" onkeypress="num_key(event)">
++ size="5" value="200" step="0.5" min="1"
++ id="centrimo_maxreg" onkeypress="num_key(event)">
+ <div class="help" onclick="help_popup(this, 'pop_centrimo_maxreg')"></div>
+
+ <h3 class="meme">Set <i>E</i>-value threshold for reporting centrally enriched regions</h3>
+ <label for="centrimo_ethresh"><i>E</i>-value ≤</label>
+ <input class="meme" type="number" name="centrimo_ethresh"
+- size="5" value="10" id="centrimo_ethresh" >
++ size="5" value="10" step="any" min="0.00000001"
++ id="centrimo_ethresh">
+ <div class="help" onclick="help_popup(this, 'pop_centrimo_ethresh')"></div>
+
+ <h3 class="meme">Include sequence IDs</h3>
+diff -r 02aa25f920a7 -r caa80f3ff934 website/cgi-bin/tomtom.tmpl
+--- a/website/cgi-bin/tomtom.tmpl Fri Oct 05 09:45:00 2012 +1000
++++ b/website/cgi-bin/tomtom.tmpl Fri Oct 05 00:26:25 2012 -0700
+@@ -233,7 +233,7 @@
+ </p>
+ </div>
+ <div class="meme">
+- <form enctype="multipart/form-data" method="POST" action="tomtom.cgi" onsubmit="return check()">
++ <form enctype="multipart/form-data" method="POST" action="tomtom.cgi" novalidate onsubmit="return check()">
+ <fieldset>
+ <legend>Data Submission Form</legend>
+ <p class="meme">Search one or more DNA motifs against a DNA motif database.</p>
+@@ -461,7 +461,7 @@
+ </select>
+ <
+ <!-- without html 5 support this is just a text field -->
+- <input type="number" name="thresh" id="thresh" class="meme" step="0.10" value="10" size="4">
++ <input type="number" name="thresh" id="thresh" class="meme" step="any" value="10" size="4">
+ <div class="help" onclick="help_popup(this, 'pop_thresh')"></div><br>
+ </div>
+ <!-- Complete scoring -->
Added: trunk/packages/meme/trunk/debian/patches/patch_4.9.0_2
===================================================================
--- trunk/packages/meme/trunk/debian/patches/patch_4.9.0_2 (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/patch_4.9.0_2 2013-01-15 11:00:22 UTC (rev 12793)
@@ -0,0 +1,317 @@
+diff -r caa80f3ff934 -r 017b59926721 doc/cite.html
+--- a/doc/cite.html Fri Oct 05 00:26:25 2012 -0700
++++ b/doc/cite.html Thu Oct 25 11:57:42 2012 -0700
+@@ -68,6 +68,15 @@
+ </div>
+ </li>
+ <li>
++ <b>CentriMo</b>
++ <div class="cite">
++ Timothy L. Bailey and Philip Machanick,
++ "Inferring direct DNA binding from ChIP-seq",
++ <i>Nucleic Acids Research</i>, <b>40</b>:e128, 2012.
++ <a href="http://nar.oxfordjournals.org/content/early/2012/05/18/nar.gks433.abstract">[Abstract and Full Text]</a>
++ </div>
++ </li>
++ <li>
+ <b>DREME</b>
+ <div class="cite">
+ Timothy L. Bailey,
+diff -r caa80f3ff934 -r 017b59926721 doc/fasta-get-markov.xml
+--- a/doc/fasta-get-markov.xml Fri Oct 05 00:26:25 2012 -0700
++++ b/doc/fasta-get-markov.xml Thu Oct 25 11:57:42 2012 -0700
+@@ -10,7 +10,7 @@
+ <div id="main">
+ <script src="./meme-suite-logo.js" type="text/javascript">></script>
+ <h1>fasta-get-markov</h1>
+- <p><b>Usage:</b> fasta-get-markov <<i>q</i>> [options]</p>
++ <p><b>Usage:</b> fasta-get-markov [options]</p>
+ <p><b>Description:</b></p>
+ <p>
+ <code>fasta-get-markov</code>
+diff -r caa80f3ff934 -r 017b59926721 doc/iupac2meme.html
+--- a/doc/iupac2meme.html Fri Oct 05 00:26:25 2012 -0700
++++ b/doc/iupac2meme.html Thu Oct 25 11:57:42 2012 -0700
+@@ -44,7 +44,9 @@
+ <dt>-bg <background file></dt><dd>file with background frequencies of letters; default: uniform background</dd>
+ <dt>-pseudo <total pseudocounts></dt><dd>add <total pseudocounts> times letter background to each frequency; default: 0</dd>
+ <dt>-logodds</dt><dd>output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only</dd>
+- <dt>-url <website></dt><dd>website for the motif; The motif name is substituted for MOTIF_NAME; default: no url</dd>
++ <dt>-url <website></dt><dd>website for the motif; a line with the tag
++ 'URL' followed by the provided website URL is added to the end of the output;
++ default: no URL line</dd>
+ </dl>
+ <p><b>Output:</b></p>
+ <p>
+diff -r caa80f3ff934 -r 017b59926721 doc/meme-install.html
+--- a/doc/meme-install.html Fri Oct 05 00:26:25 2012 -0700
++++ b/doc/meme-install.html Thu Oct 25 11:57:42 2012 -0700
+@@ -64,10 +64,13 @@
+ printed by the configure command.
+ <br /><span class="command">$ tar zxf meme_VERSION.tar.gz</span>
+ <br /><span class="command">$ cd meme_VERSION</span>
+- <br /><span class="command">$ ./configure --prefix=$home/meme --with-url=http://meme.nbcr.net/meme</span>
++ <br /><span class="command">$ ./configure --prefix=$HOME/meme --with-url=http://meme.nbcr.net/meme</span>
++ <br /><span class="command">$ make</span>
++ <br /><span class="command">$ make test</span>
++ <br /><span class="command">$ make install</span>
+ </li>
+ <li>Edit your shell configuration file to add
+- <br /><span class="command">$home/meme/bin</span>
++ <br /><span class="command">$HOME/meme/bin</span>
+ to your shell's path.
+ </li>
+ </ol>
+@@ -83,7 +86,7 @@
+ </li>
+ <li>
+ This will overwrite any previously existing
+- <span class="command">$home/meme</span> directory
++ <span class="command">$HOME/meme</span> directory
+ you may have. You can set the directory to something different in
+ the <span class="command">configure</span> command using the
+ <span class="command">--prefix</span> option.
+diff -r caa80f3ff934 -r 017b59926721 etc/centrimo_graph.js
+--- a/etc/centrimo_graph.js Fri Oct 05 00:26:25 2012 -0700
++++ b/etc/centrimo_graph.js Thu Oct 25 11:57:42 2012 -0700
+@@ -498,7 +498,7 @@
+ length = this.end - this.start;
+ tick_max = length / 2;
+ nticks = 5;
+- tick_inc = Math.round(tick_max / (10*nticks)) * 10;
++ tick_inc = Math.max(1, Math.round(tick_max / (10*nticks))) * 10;
+ scale_x = w / length;
+ ctx.beginPath();
+ ctx.moveTo(0.5, -5);
+diff -r d1cae7820408 -r 3b69fb53ef3e src/binomial.c
+--- a/src/binomial.c Mon Oct 29 12:30:07 2012 -0700
++++ b/src/binomial.c Tue Nov 06 14:53:23 2012 +1000
+@@ -80,7 +80,11 @@
+ h *= del;
+ if (fabs(del - 1.0) < EPS) break; // Are we done?
+ }
+- if (m > MAXIT) fprintf(stderr, "a or b too big, or MAXIT too small in betacf");
++ if (m > MAXIT) {
++ fprintf(stderr, "a (%g) or b (%g) too big, or MAXIT (%d) too small in"
++ " betacf. Input x is %g. Returning %g.\n",
++ a, b, MAXIT, x, h);
++ }
+ return h;
+ }
+
+diff -r d1cae7820408 -r 3b69fb53ef3e src/glam2_glam2.c
+--- a/src/glam2_glam2.c Mon Oct 29 12:30:07 2012 -0700
++++ b/src/glam2_glam2.c Tue Nov 06 14:53:23 2012 +1000
+@@ -1,13 +1,14 @@
+ /* GLAM2 */
+ #include <assert.h>
+ #include <float.h> /* DBL_MIN, DBL_EPSILON */
++#include <sys/wait.h> /* WEXITSTATUS and associated macros */
+ #include "glam2_util.h"
+ #include "glam2_glam2.h"
+ #include "glam2_init.h"
+ #include "glam2_output.h"
+ #include "glam2_site_sample.h"
+ #include "glam2_column_sample.h"
+-#include "dir.h" // MEME specific distribution
++#include "utils.h"
+
+ VERBOSE_T verbosity; // needed by meme utilities
+
+@@ -144,6 +145,27 @@
+ return x < y ? +1 : x > y ? -1 : 0;
+ }
+
++inline void report_external_failure(const char *prog, int status) {
++ if (status == 0) {
++ // success
++ } if (status == -1) {
++ fprintf(stderr, "Program %s was not run due to a system error\n", prog);
++ } else if (WIFEXITED(status)) {
++ if (WEXITSTATUS(status) == 127) {
++ // shell error, maybe the program couldn't be found?
++ // the shell already prints out a message when this happens
++ } else {
++ fprintf(stderr, "Program %s exited with value %d\n", prog, WEXITSTATUS(status));
++ }
++ } else if (WIFSIGNALED(status)) {
++ fprintf(stderr, "Program %s died from signal %d, %s coredump\n", prog,
++ WTERMSIG(status), (WCOREDUMP(status) ? "with" : "without"));
++ } else {
++ fprintf(stderr, "Unknown error running %s, system returned status %d\n",
++ prog, status);
++ }
++}
++
+ int main(int argc, char **argv) {
+ data d;
+ glam2_aln *alns;
+@@ -186,21 +208,29 @@
+ xfclose(d.out); // close text output file
+
+ // Create the HTML output and MEME format output
+- // This depends on variable "MEME_DIR" containing the
+- // path to the installation directory.
+- int command_length = strlen(MEME_DIR) + strlen(d.txt_filename) +
+- strlen(d.html_filename) + 50;
+- char *command = xmalloc(command_length);
+- sprintf(command, "%s/bin/glam2html < %s > %s",
+- MEME_DIR, d.txt_filename, d.html_filename);
+- if (!system(command)) {
++ char *glam2html, *glam2psfm, *command;
++ int command_length, command_ret;
++ // create the paths to the programs
++ glam2html = make_path_to_file(get_meme_bin_dir(), "glam2html");
++ glam2psfm = make_path_to_file(get_meme_bin_dir(), "glam2psfm");
++ // allocate memory for the command
++ command_length = strlen(glam2html) + strlen(d.txt_filename) + strlen(d.html_filename) + 50;
++ command = xmalloc(command_length);
++ // run glam2html
++ sprintf(command, "%s < %s > %s", glam2html, d.txt_filename, d.html_filename);
++ if ((command_ret = system(command)) != 0) {
++ report_external_failure("glam2html", command_ret);
+ fprintf(stderr, "Warning: failed to convert output to HTML!\n");
+ }
+- sprintf(command, "%s/bin/glam2psfm < %s > %s",
+- MEME_DIR, d.txt_filename, d.psfm_filename);
+- if (system(command) != 0) {
++ // run glam2psfm
++ sprintf(command, "%s < %s > %s", glam2psfm, d.txt_filename, d.psfm_filename);
++ if ((command_ret = system(command)) != 0) {
++ report_external_failure("glam2psfm", command_ret);
+ fprintf(stderr, "Warning: failed to convert output to MEME format motif!\n");
+ }
++ free(command);
++ free(glam2psfm);
++ free(glam2html);
+
+ return 0;
+ }
+diff -r d1cae7820408 -r 3b69fb53ef3e src/init.c
+--- a/src/init.c Mon Oct 29 12:30:07 2012 -0700
++++ b/src/init.c Tue Nov 06 14:53:23 2012 +1000
+@@ -20,9 +20,10 @@
+ #include "meme.h"
+ #include "general.h"
+ #include "banner.h"
+-#include "dir.h"
++#include <string.h>
+ #include <sys/types.h>
+ #include <unistd.h>
++#include "utils.h"
+ #include "io.h"
+ #include "psp.h"
+
+@@ -51,7 +52,6 @@
+ static char *default_output_dirname = "meme_out"; /* default name of output
+ directory */
+ static BOOLEAN clobber = FALSE; /* default is not to overwrite existing files */
+-static char *plib_name = NULL; /* use default library */
+ static char *mod = "zoops"; /* model type input string; default ZOOPS */
+ static char *alph = "PROTEIN"; /* default alphabet IUPAC protein 1-letter */
+ static BOOLEAN revcomp = FALSE; /* don't use reverse complement strand of DNA */
+@@ -105,7 +105,6 @@
+ static int maxsize= 100000; /* dataset size limit */
+ static int seed = 0; /* random number seed */
+ static double seqfrac = 1; /* fraction of input dataset sequences to use */
+-static char *meme_directory = NULL; /* meme source directory */
+ static double max_time = 0; /* maximum allowed CPU time; ignore if 0 */
+
+ /*
+@@ -156,6 +155,7 @@
+ DATASET *dataset=NULL, *neg_dataset=NULL;
+ double evt = BIG; /* no E-value cutoff */
+ BOOLEAN no_print = FALSE; /* turn off printing if parallel and not main */
++ char *plib_name = NULL; /* use default library */
+
+ #ifdef PARALLEL
+ /* turn off printing if parallel and not the main processor */
+@@ -242,7 +242,7 @@
+ prior = _OPTION_);
+ DATA_OPTN(1, b, <b>, \t\tstrength of the prior, beta = atof(_OPTION_));
+ DATA_OPTN(1, plib, <plib>, \t\tname of Dirichlet prior file,
+- plib_name = _OPTION_);
++ plib_name = strdup(_OPTION_));
+ DATA_OPTN(1, spfuzz, <spfuzz>, \tfuzziness of sequence to theta mapping,
+ map_scale = atof(_OPTION_));
+ DATA_OPTN(1, spmap, uni|pam, \tstarting point seq to theta mapping type,
+@@ -342,11 +342,6 @@
+ exit(1);
+ }
+
+- /* get the name of the directory where MEME is installed */
+- if (!meme_directory) { /* not given on command line */
+- meme_directory = MEME_DIR;
+- }
+-
+ /* get the objective function type */
+ if (!strcmp(obj, "pv")) {
+ objfun = Pv;
+@@ -488,16 +483,11 @@
+ if (ptype == Dmix || ptype == Mega || ptype == MegaP) {
+ /* make the name of the prior library */
+ if (!plib_name) {
+- char *tmp1, *tmp2;
+- if (!strcmp(alphabet, PROTEIN0)) {
+- plib_name = PROTEIN_PLIB; /* default mixture prior for proteins */
+- } else {
+- plib_name = DNA_PLIB; /* default mixture prior for DNA */
++ if (!strcmp(alphabet, PROTEIN0)) {/* default mixture prior for proteins */
++ plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB);
++ } else {/* default mixture prior for DNA */
++ plib_name = make_path_to_file(get_meme_etc_dir(), DNA_PLIB);
+ }
+- /* prepend meme_directory to file name */
+- Strcat(tmp1, meme_directory, "/etc/");
+- Strcat(tmp2, tmp1, plib_name);
+- plib_name = tmp2;
+ }
+ }
+ if ((ptype == Mega || ptype == MegaP) && beta == -1) {
+@@ -869,9 +859,9 @@
+ dataset->seqfrac = seqfrac;
+ /* save name of prior library */
+ if (plib_name) {
+- dataset->plib_name = plib_name + strlen(plib_name);
+- while (*dataset->plib_name != '/') dataset->plib_name--;
+- dataset->plib_name++; /* strip off directory */
++ char *tmp, *base; // remove the directory, leaving just the file name
++ for (tmp = base = plib_name; *tmp; tmp++) if (*tmp == '/') base = tmp + 1;
++ dataset->plib_name = strdup(base); // copy the name
+ } else {
+ dataset->plib_name = NULL;
+ }
+@@ -912,6 +902,9 @@
+ banner("MEME", *text_output);
+ fprintf(*text_output, "\n\n");
+
++ /* cleanup */
++ free(plib_name);
++
+ } /* init_meme */
+
+ /***************************************************************************/
+diff -r d1cae7820408 -r 3b69fb53ef3e src/utils.c
+--- a/src/utils.c Mon Oct 29 12:30:07 2012 -0700
++++ b/src/utils.c Tue Nov 06 14:53:23 2012 +1000
+@@ -650,7 +650,7 @@
+ }
+ regfree(&re_evalue);
+ regfree(&re_inf);
+- if (myerrno) errno = myerrno;
++ errno = myerrno;
+ return log_ev;
+ }
+
+diff -r d1cae7820408 -r 3b69fb53ef3e website/html/fimo-intro.html
+--- a/website/html/fimo-intro.html Mon Oct 29 12:30:07 2012 -0700
++++ b/website/html/fimo-intro.html Tue Nov 06 14:53:23 2012 +1000
+@@ -111,7 +111,7 @@
+ (<a href="doc/examples/fimo_example_output_files/fimo.xml">example</a>)</li>
+ <li><a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml">GFF</a>
+ (<a href="doc/examples/fimo_example_output_files/fimo.gff">example</a>)</li>
+- <li>Plain text (<a href="doc/examples/fimo_example_output_files/fimo.gff">example</a>)</li>
++ <li>Plain text (<a href="doc/examples/fimo_example_output_files/fimo.txt">example</a>)</li>
+ </ul>
+ <script type="text/javascript">make_footer('');</script>
+ </div>
Added: trunk/packages/meme/trunk/debian/patches/readme_patchlevel.html
===================================================================
--- trunk/packages/meme/trunk/debian/patches/readme_patchlevel.html (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/readme_patchlevel.html 2013-01-15 11:00:22 UTC (rev 12793)
@@ -0,0 +1,154 @@
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset='utf-8'>
+ <title>MEME Suite 4.9.0 Patches</title>
+ <style>
+ textarea {
+ width: 100%;
+ display: block;
+ }
+ table, th, td {
+ border: 1px solid black;
+ border-collapse: collapse;
+ }
+ td, th {
+ padding: 0 5px;
+ }
+ </style>
+ </head>
+ <body>
+ <h3>MEME Suite 4.9.0 Patches</h3>
+ <p>This file gives notes and installation instructions for patches of
+ the MEME Suite version 4.9.0.</p>
+
+ <p>The patches should always be installed in order because
+ later patches may depend on changes made in earlier patches.</p>
+ <table>
+ <tr>
+ <th>Patch</th><th>Notes</th><th>Download</th>
+ </tr>
+ <tr>
+ <td>1</td>
+ <td><a href="#patch1">notes</a></td>
+ <td><a href="patch_4.9.0_1">download</a></td>
+ </tr>
+ <tr>
+ <td>2</td>
+ <td><a href="#patch2">notes</a></td>
+ <td><a href="patch_4.9.0_2">download</a></td>
+ </tr>
+ </table>
+ <p>If you're patching a fresh MEME install then all the patches can be
+ installed by:
+ <ol>
+ <li>Downloading all the patch files (linked above) to the root of the
+ MEME Suite source distribution</li>
+ <li>Changing your working directory to the root of the MEME Suite source distribution</li>
+ <li>Running the command
+ <textarea rows="2" readonly>patch -p1 -i patch_4.9.0_1
+patch -p1 -i patch_4.9.0_2</textarea>
+ </li>
+ <li>If nothing went wrong then install the changes with the command
+ <textarea rows="1" readonly>make install</textarea></li>
+ </ol>
+
+<p>Contact <a href="mailto:MEME Support<meme at nbcr.net>">meme at nbcr.net</a>
+if you run into problems.</p>
+<hr>
+
+<h4 id="patch1">Patch 1</h4>
+<a href="patch_4.9.0_1">Download</a>
+
+<p>This patch fixes the following:
+<ul>
+ <li>Users of the Google Chrome browser could not submit jobs to MEME-ChIP
+ because Chrome's validation of number type inputs by default only allow
+ integers. This has been fixed by specifying the 'any' option for the step
+ field and by turning off Chrome's automatic validation.</li>
+ <li>The server-side validation on MEME-ChIP's page was broken for some
+ fields.</li>
+</ul>
+
+<p>To apply this patch, download the patch file to the root of the MEME Suite source distribution,
+change your working directory to the root of the MEME Suite source distribution and
+run the command:</p>
+<textarea rows="1" readonly>patch -p1 -i patch_4.9.0_1</textarea>
+
+
+<p>You should see the following message:</p>
+<textarea rows="6" readonly>patching file etc/centrimo_template.html
+patching file website/cgi-bin/centrimo.tmpl
+patching file website/cgi-bin/dreme.tmpl
+patching file website/cgi-bin/meme-chip.pl
+patching file website/cgi-bin/meme-chip.tmpl
+patching file website/cgi-bin/tomtom.tmpl</textarea>
+
+<p>Now run:</p>
+<textarea rows="2" readonly>cd scripts
+make install</textarea>
+
+<p>This will copy the change from the source directory to the installed version of the
+MEME Suite web server.</p>
+
+<p>Contact <a href="mailto:MEME Support<meme at nbcr.net>">meme at nbcr.net</a>
+if you run into problems.</p>
+
+<hr>
+
+<h4 id="patch2">Patch 2</h4>
+<a href="patch_4.9.0_2">Download</a>
+
+<p>This patch fixes the following:
+<ul>
+ <li>Added a citation for CentriMo to the main citation page.</li>
+ <li>Uppercased the $home environment variable to $HOME in the installation
+ documentation. The original $home was for the default for c shell which is now very
+ uncommon and the more common Bash uses $HOME instead.</li>
+ <li>Fixed a bug in the CentriMo graphing code which could cause an infinite loop
+ and lock up the webpage.</li>
+ <li>Changed the description of the <code>-url</code> option in the iupac2meme
+ documentation.</li>
+ <li>Fixed the fasta-get-markov usage line by removing a incorrect parameter.</li>
+ <li>Changed the quick install guide to mention running <code>make</code>,
+ <code>make test</code>, <code>make install</code>.</li>
+ <li>Improved error reporting for binomial calculations.</li>
+ <li>Fixed an incorrect check that was causing GLAM2 to print a warning about
+ failing to create HTML output when nothing was wrong.</li>
+ <li>Changed access of external programs and resources from MEME and GLAM2 to
+ check the environment variables $MEME_BIN_DIR and $MEME_ETC_DIR before
+ resorting to the configured default.</li>
+ <li>Fixed motif reading code that was rejecting E-values of "0.00e+00".</li>
+ <li>Fixed broken link to sample FIMO text file.</li>
+</ul>
+
+<p>To apply this patch, download the patch file to the root of the MEME Suite source distribution,
+change your working directory to the root of the MEME Suite source distribution and
+run the command:</p>
+<textarea rows="1" readonly>patch -p1 -i patch_4.9.0_2</textarea>
+
+
+<p>You should see the following message:</p>
+<textarea rows="10" readonly>patching file doc/cite.html
+patching file doc/fasta-get-markov.xml
+patching file doc/iupac2meme.html
+patching file doc/meme-install.html
+patching file etc/centrimo_graph.js
+patching file src/binomial.c
+patching file src/glam2_glam2.c
+patching file src/init.c
+patching file src/utils.c
+patching file website/html/fimo-intro.html</textarea>
+
+<p>Now run:</p>
+<textarea rows="1" readonly>make install</textarea>
+
+<p>This will copy the change from the source directory to the installed version of the
+MEME Suite web server.</p>
+
+<p>Contact <a href="mailto:MEME Support<meme at nbcr.net>">meme at nbcr.net</a>
+if you run into problems.</p>
+
+<hr>
+ </body>
+</html>
Modified: trunk/packages/meme/trunk/debian/patches/series
===================================================================
--- trunk/packages/meme/trunk/debian/patches/series 2013-01-14 15:31:34 UTC (rev 12792)
+++ trunk/packages/meme/trunk/debian/patches/series 2013-01-15 11:00:22 UTC (rev 12793)
@@ -1,5 +1,7 @@
+patch_4.9.0_1
+patch_4.9.0_2
fix_doc_location
no_libxml_configure
fix_installer_paths
-fix_plib_path
+#broken and most probably unneeded, see Remark inside the file# fix_plib_path
perl-include.patch
Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules 2013-01-14 15:31:34 UTC (rev 12792)
+++ trunk/packages/meme/trunk/debian/rules 2013-01-15 11:00:22 UTC (rev 12793)
@@ -53,6 +53,7 @@
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs
-
-
-
+ cd ../tarballs; \
+ wget -r --no-directories --no-parent -l2 ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/patches \
+ rm -f .r.html
+ echo "Make sure you use the downloaded patches `ls ../tarballs/patch_*` as quilt patch and use the proper patch level in package version in debian/copyright."
More information about the debian-med-commit
mailing list