[med-svn] r19061 - trunk/packages/murasaki/trunk/debian

[Andreas Tille]

Author: tille
Date: 2015-04-15 13:15:21 +0000 (Wed, 15 Apr 2015)
New Revision: 19061

Added:
   trunk/packages/murasaki/trunk/debian/docs
   trunk/packages/murasaki/trunk/debian/manpages
Modified:
   trunk/packages/murasaki/trunk/debian/README.Debian
   trunk/packages/murasaki/trunk/debian/install
   trunk/packages/murasaki/trunk/debian/rules
Log:
Slightly better package


Modified: trunk/packages/murasaki/trunk/debian/README.Debian
===================================================================
--- trunk/packages/murasaki/trunk/debian/README.Debian	2015-04-15 12:47:39 UTC (rev 19060)
+++ trunk/packages/murasaki/trunk/debian/README.Debian	2015-04-15 13:15:21 UTC (rev 19061)
@@ -1,65 +1,10 @@
 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
 
+Here you can find some example data to test murasaki:
 
-Getting started
----------------
+   http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Whole%20Genome%20Alignments
 
-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 
+ -- Andreas Tille <tille at debian.org>  Wed, 15 Apr 2015 14:06:19 +0200
 
-    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/docs
===================================================================
--- trunk/packages/murasaki/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/murasaki/trunk/debian/docs	2015-04-15 13:15:21 UTC (rev 19061)
@@ -0,0 +1,2 @@
+doc/*.html
+doc/*.txt

Modified: trunk/packages/murasaki/trunk/debian/install
===================================================================
--- trunk/packages/murasaki/trunk/debian/install	2015-04-15 12:47:39 UTC (rev 19060)
+++ trunk/packages/murasaki/trunk/debian/install	2015-04-15 13:15:21 UTC (rev 19061)
@@ -1,10 +1,9 @@
-*.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
+*.p[lm]			usr/share/perl5/murasaki
+debian/config.pl	usr/share/perl5/murasaki
+perlmodules/*		usr/share/perl5/murasaki
+geneparse		usr/bin
+mbfa			usr/bin
+murasaki		usr/bin
+cgr-*			usr/lib/murasaki
+testeco			usr/lib/murasaki
+align-*			usr/lib/murasaki

Added: trunk/packages/murasaki/trunk/debian/manpages
===================================================================
--- trunk/packages/murasaki/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/murasaki/trunk/debian/manpages	2015-04-15 13:15:21 UTC (rev 19061)
@@ -0,0 +1 @@
+doc/*.1

Modified: trunk/packages/murasaki/trunk/debian/rules
===================================================================
--- trunk/packages/murasaki/trunk/debian/rules	2015-04-15 12:47:39 UTC (rev 19060)
+++ trunk/packages/murasaki/trunk/debian/rules	2015-04-15 13:15:21 UTC (rev 19061)
@@ -3,12 +3,5 @@
 # Copyright 2008 Andreas Tille
 # GPL
 
-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)
-
 %:
 	dh $@