[med-svn] r13870 - trunk/packages/mira/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-06-07 09:13:22 +0000 (Fri, 07 Jun 2013)
New Revision: 13870

Added:
   trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1
Modified:
   trunk/packages/mira/trunk/debian/changelog
   trunk/packages/mira/trunk/debian/mira-assembler.manpages
Log:
debian/miraSearchESTSNPs.1: Wrote manpage but mention that this functionality is deactivated in version 3.9.17
debian/mira-assembler.manpages: Simply install all manpages that can be found


Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog	2013-06-07 09:10:54 UTC (rev 13869)
+++ trunk/packages/mira/trunk/debian/changelog	2013-06-07 09:13:22 UTC (rev 13870)
@@ -24,6 +24,10 @@
   * debian/{mira.1,miradiff.1,miramer.1, scftool.1, convert_project.1,
     fasta2frag.1, fast[aq]select.1, fastatool.1}:
     Wrote manpage for some programs
+  * debian/miraSearchESTSNPs.1: Wrote manpage but mention that this
+    functionality is deactivated in version 3.9.17
+  * debian/mira-assembler.manpages: Simply install all manpages that can be
+    found
   * Removed debian/obsolete.mira-assembler.install
   * debian/control: The actual scripts do not contain the .tcl suffix
     in our installation

Modified: trunk/packages/mira/trunk/debian/mira-assembler.manpages
===================================================================
--- trunk/packages/mira/trunk/debian/mira-assembler.manpages	2013-06-07 09:10:54 UTC (rev 13869)
+++ trunk/packages/mira/trunk/debian/mira-assembler.manpages	2013-06-07 09:13:22 UTC (rev 13870)
@@ -1,8 +1 @@
-debian/convert_project.1
-debian/fasta2frag.1
-debian/fastaselect.1
-debian/fastatool.1
-debian/fastqselect.1
-debian/miradiff.1
-debian/miramer.1
-debian/scftool.1
+debian/*.1

Added: trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1
===================================================================
--- trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1	                        (rev 0)
+++ trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1	2013-06-07 09:13:22 UTC (rev 13870)
@@ -0,0 +1,43 @@
+.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains
+.SH DESCRIPTION
+The program miraSearchESTSNPs can be used for assembly of EST data from
+different strains (or organisms) and SNP detection within this assembly.
+This is the former miraEST program which was renamed as many people got
+confused regarding whether to use MIRA in est mode or miraEST. 
+.PP
+miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA
+transcript sequences gathered in EST sequencing projects of more than
+one strain, which can be a reliable basis for subsequent analysis steps
+like clustering or exon analysis. This means that even genes that
+contain only one transcribed SNP on different alleles are first treated
+as different transcripts. The optional last step of the assembly process
+can be configured as a simple clusterer that can assemble transcripts
+containing the same exon sequence -- but only differ in SNP positions --
+into one consensus sequence. Such SNPs can then be analysed, classified
+and reliably assigned to their corresponding mRNA transcriptome
+sequence. However, it is important to note that miraSearchESTSNPs is an
+assembler and not a full blown clustering tool. 
+.SH SYNOPSIS
+In version 3.9.17 this functionality is deactivated.
+.SH "SEE ALSO"
+A more extensive documentation is provided in the mira-doc package and can be found at
+/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
+.PP
+You can also subscribe one of the MIRA mailing lists at
+.IP
+http://www.chevreux.org/mira_mailinglists.html
+.PP
+After subscribing, mail general questions to the MIRA talk mailing list:
+.IP
+mira_talk at freelists.org
+.SH BUGS
+To report bugs or ask for features, please use the new ticketing system at:
+.IP
+http://sourceforge.net/apps/trac/mira\-assembler/
+.SH AUTHOR
+The author of the mira code is Bastien Chevreux <bach at chevreux.org>
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.