[med-svn] r2705 - trunk/packages/theseus/trunk/debian

[mok0-guest at alioth.debian.org]

Author: mok0-guest
Date: 2008-11-18 22:17:16 +0000 (Tue, 18 Nov 2008)
New Revision: 2705

Added:
   trunk/packages/theseus/trunk/debian/README.Debian
Modified:
   trunk/packages/theseus/trunk/debian/getexamples
   trunk/packages/theseus/trunk/debian/theseus_align.1
Log:
README.Debian file added, explaining the peculiarity of the 
get-orig-source target. The theseus_align.1 manpage has been
expanded, and the getexamples script updated.


Added: trunk/packages/theseus/trunk/debian/README.Debian
===================================================================
--- trunk/packages/theseus/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/theseus/trunk/debian/README.Debian	2008-11-18 22:17:16 UTC (rev 2705)
@@ -0,0 +1,40 @@
+== README.Debian ==
+
+
+The theseus_align script
+------------------------
+
+This package includes the script theseus_align, which is distributed by
+the upstream author at his website. The script used to be a part of the
+distributed tarball, but was removed to avoid having to include it in 
+the various binary distribution tarballs.
+
+Rather than preparing a separate package only containing the shell script 
+theseus_align, we have chosen to include it in this package, along with
+its manpage.
+
+There is no good way of doing this. We have chosen to wget the script and 
+place it in debian/ from where it will be installed. Similarly, we
+provide a manpage, also in debian/.
+
+We provide a target "get-orig-source" in debian/rules to fetch the script
+and edit it for standard file locations and place it in debian/. We are 
+not very happy about this solution, but at least it works.
+
+The script is installed in /usr/bin, hardwired with the alignment program 
+muscle. It is posible to use other programs with theseus_align; in case 
+you wants to do this, copy the script to a local area and edit it.
+
+
+The getexamples script
+----------------------
+
+The getexamples script, found in /usr/share/doc/theseus/examples/, 
+illustrates how data can be retrieved from PDB and Astral services, 
+for subsequent analysis with theseus.
+
+Note that some of the data files found in examples/, have a different
+SCOP-sid in the most recent release of the Astral database.
+
+
+ -- Morten Kjeldgaard <mok0 at ubuntu.com>, Tue, 18 Nov 2008 23:14:32 +0100

Modified: trunk/packages/theseus/trunk/debian/getexamples
===================================================================
--- trunk/packages/theseus/trunk/debian/getexamples	2008-11-17 23:14:32 UTC (rev 2704)
+++ trunk/packages/theseus/trunk/debian/getexamples	2008-11-18 22:17:16 UTC (rev 2705)
@@ -21,26 +21,29 @@
 
 pdbs="1s40"
 
-astrals="d1cih__ d1cih__2 d1crj__ d1csu__ d1csx__ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeb__ d2pcbb_"
+astrals="d1ciha_ d1crja_ d1csua_ d1csxa_ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeba_ d2pcbb_"
+#astrals="d1cih__ d1cih__2 d1crj__ d1csu__ d1csx__ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeb__ d2pcbb_"
 
 # function to fetch entries from the pdb
 pdb_fetch () {
   for f in $* ; do
-      wget -nv http://www.pdb.org/pdb/files/$f.pdb.gz 
-      gzip -dc $f.pdb.gz > $f.pdb
+      wget -q -O $f.pdb.gz ftp://ftp.wwpdb.org:/pub/pdb/data/structures/all/pdb/pdb${f}.ent.gz 
+      gzip -d ${f}.pdb.gz
+      echo fetched $f.pdb
   done
 }
 
 # function to fetch entries from astral
 astral_fetch() {
   for f in $* ; do
-    wget -nv http://astral.berkeley.edu/pdbstyle.cgi?id=${f}.pdb&output=text
+    wget -q -O ${f}.pdb http://astral.berkeley.edu/pdbstyle.cgi?id=${f}&output=text 
+    echo fetched $f.pdb
   done
 }
 
 savedir=$PWD
 cd /tmp
-
+echo Downloading to directory /tmp
 pdb_fetch $pdbs
 astral_fetch $astrals
 

Modified: trunk/packages/theseus/trunk/debian/theseus_align.1
===================================================================
--- trunk/packages/theseus/trunk/debian/theseus_align.1	2008-11-17 23:14:32 UTC (rev 2704)
+++ trunk/packages/theseus/trunk/debian/theseus_align.1	2008-11-18 22:17:16 UTC (rev 2705)
@@ -54,7 +54,16 @@
 programs mentioned above, you'll have to copy the script to your own
 directory and edit it.
 .SH SEE ALSO
-\fBtheseus\fR (1), \fBclustalw\fR (1) 
+\fBtheseus\fR (1), 
+\fBmuscle\fR (1),
+\fBclustalw\fR (1),
+\fBt_coffee\fR (1),
+\fBkalign\fR (1),
+\fBdialign2\fR (1),
+\fBmafft\fR (1).
+All of these programs can be installed on Debian or Ubuntu systems using 
+\fBapt-get\fR (8).
+
 .SH AUTHOR
 \fBtheseus_align\fR was written by Douglas L. Theobald, Department of
 Biochemistry, Brandeis University.