[med-svn] r1794 - trunk/packages/murasaki/trunk/debian

Fri Apr 18 10:01:02 UTC 2008

Author: tille
Date: 2008-04-18 10:01:00 +0000 (Fri, 18 Apr 2008)
New Revision: 1794

Added:
   trunk/packages/murasaki/trunk/debian/README.Debian
   trunk/packages/murasaki/trunk/debian/config.pl
   trunk/packages/murasaki/trunk/debian/install
Removed:
   trunk/packages/murasaki/trunk/debian/dirs
   trunk/packages/murasaki/trunk/debian/docs
Modified:
   trunk/packages/murasaki/trunk/debian/control
   trunk/packages/murasaki/trunk/debian/rules
Log:
Works up to the point where files are moved to /usr/lib/murasaki and /usr/share/perl5/murasaki; but needs definitely help to make this bunch of Perl scripts somehow handy;  need HELP from people with perl experience how to cope with this ...


Added: trunk/packages/murasaki/trunk/debian/README.Debian
===================================================================

--- trunk/packages/murasaki/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/murasaki/trunk/debian/README.Debian	2008-04-18 10:01:00 UTC (rev 1794)
@@ -0,0 +1,65 @@
+Murasaki for Debian
+-------------------
+
+Because there is no really good documentation available here is a
+quote from the website
+   http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki
+
+
+Getting started
+---------------
+
+Most of the documentation for Murasaki currently exists inside the
+various programs. You can find out what any command does by running it
+with the "--help" option. For example 
+
+    murasaki --help
+
+lists how to run Murasaki. It's long, so you might want to use
+"murasaki --help | less".
+
+An example Murasaki run might go like this:
+
+ murasaki seq/MtC.gbk seq/Mle.gbk -p[28:36] -H2 -b24 --name myalignment
+
+Runs the core alignment program. "seq/MtC.gbk seq/Mle.gbk" specifies
+the input sequences. "-p[28:36]" uses a random string consiting of 28
+1's and 8 0's. -H2 specifies to include anchor component information
+(for calculation of tf-idf scores by filter.pl). -b24 specifies to use
+only 24bit hash keys (as opposed to the default 26). This is desriable
+(possibly necessary) for machines with limited RAM. --name obviously
+the output file prefix.
+
+ simplegraph.pl output/myalignment.anchors
+
+This generates (in this case 1) graph of the anchors produced. For
+multiple alignments this outputs all pairings of the component
+sequences.
+
+ filter.pl --kogfile COG output/myalignment.anchors --rocr --dumpstats tfidf
+
+--kogfile specifies where to find reference COG data for calculating
+sensitivity and specificity. For this case (comparing MtC and Mle)
+this can be downloaded from NCBI's COGs website. --rocr generates ROC
+plots using R and ROCR. "--dumpstats tfidf" dumps the generated tf-idf
+scores to a separate file which can be read by GMV.
+
+Obviously this is just a sample run. You're strongly encouraged to
+read the documentation for each command. Murasaki includes a great
+deal of functionality without the need to write any custom scripts.
+
+
+Sample alignments
+-----------------
+
+As an example of some of the huge alignments Murasaki is capable of,
+you can download the complete set of our whole genome mammalian
+alignments here. Be aware, however, that these alignments can be huge
+(for example, murasaki-mammals.tar.gz contains the Human-Mouse-Rat,
+Human-Chimp-Rhesus, and Human-Mouse alignments, and is a 340MB
+download which decompresses into about 1GB of files), and you may have
+to edit the .seq files to point to the correct data files (and
+download them from ensembl or UCSC Genome Browser.
+
+ -- Andreas Tille <tillea at rki.de>, Fri, 18 Apr 2008 11:33:00 +0200
+

Added: trunk/packages/murasaki/trunk/debian/config.pl
===================================================================
--- trunk/packages/murasaki/trunk/debian/config.pl	                        (rev 0)
+++ trunk/packages/murasaki/trunk/debian/config.pl	2008-04-18 10:01:00 UTC (rev 1794)
@@ -0,0 +1,5 @@
+#!/usr/bin/perl
+#config file for the murasaki perl scripts
+
+our $root='/usr/lib/perl5/murasaki';
+our $seqhome="/var/lib/murasaki/seq";

Modified: trunk/packages/murasaki/trunk/debian/control
===================================================================
--- trunk/packages/murasaki/trunk/debian/control	2008-04-18 09:09:19 UTC (rev 1793)
+++ trunk/packages/murasaki/trunk/debian/control	2008-04-18 10:01:00 UTC (rev 1794)
@@ -6,7 +6,7 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 5), cdbs,
  libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev,
- libpstreams-dev
+ libterm-readkey-perl, libtext-wrapper-perl,
 Standards-Version: 3.7.3
 Homepage: http://murasaki.dna.bio.keio.ac.jp/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/murasaki/trunk/?rev=0&sc=0

Deleted: trunk/packages/murasaki/trunk/debian/dirs
===================================================================
--- trunk/packages/murasaki/trunk/debian/dirs	2008-04-18 09:09:19 UTC (rev 1793)
+++ trunk/packages/murasaki/trunk/debian/dirs	2008-04-18 10:01:00 UTC (rev 1794)
@@ -1,2 +0,0 @@
-usr/bin
-usr/sbin

Deleted: trunk/packages/murasaki/trunk/debian/docs
===================================================================

Added: trunk/packages/murasaki/trunk/debian/install
===================================================================
--- trunk/packages/murasaki/trunk/debian/install	                        (rev 0)
+++ trunk/packages/murasaki/trunk/debian/install	2008-04-18 10:01:00 UTC (rev 1794)
@@ -0,0 +1,10 @@
+*.p[lm]          usr/share/perl5/murasaki
+debian/config.pl usr/share/perl5/murasaki
+cgr-image        usr/lib/murasaki
+cgr-compare      usr/lib/murasaki
+cgr-random       usr/lib/murasaki
+cgr-sample       usr/lib/murasaki
+testeco          usr/lib/murasaki
+align-compare    usr/lib/murasaki
+align-or         usr/lib/murasaki
+geneparse        usr/lib/murasaki

Modified: trunk/packages/murasaki/trunk/debian/rules
===================================================================
--- trunk/packages/murasaki/trunk/debian/rules	2008-04-18 09:09:19 UTC (rev 1793)
+++ trunk/packages/murasaki/trunk/debian/rules	2008-04-18 10:01:00 UTC (rev 1794)
@@ -7,5 +7,9 @@
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
 
-INCLUDEDIRS = -I./include -I/usr/include/pstream
+INCLUDEDIRS = -I./include 
+## Murasaki provides local pstream header file which somehow sucks but
+## it seems safer to use this than libpstreams-dev BUild-Depends and
+## INCLUDEDIRS = -I/usr/include/pstream
+
 CFLAGS += $(INCLUDEDIRS)


