[med-svn] r22121 - in trunk/packages/profbval/trunk/debian: . tests

[Tatiana Malygina]

Author: latticetower-guest
Date: 2016-06-09 16:53:38 +0000 (Thu, 09 Jun 2016)
New Revision: 22121

Added:
   trunk/packages/profbval/trunk/debian/README.test
   trunk/packages/profbval/trunk/debian/docs
Modified:
   trunk/packages/profbval/trunk/debian/changelog
   trunk/packages/profbval/trunk/debian/tests/installation-test
Log:
added d/README.test, d/docs, improved testsuite

Added: trunk/packages/profbval/trunk/debian/README.test
===================================================================
--- trunk/packages/profbval/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/profbval/trunk/debian/README.test	2016-06-09 16:53:38 UTC (rev 22121)
@@ -0,0 +1,53 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by executing
+
+    sh installation-test
+
+in order to confirm its integrity.
+
+To test manually, cd to some dir where you have write permissions and do
+ 
+    cp -a /usr/share/doc/profbval/examples/* .
+    profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp result.profbval 9 6
+
+There is also cad23.profbval.gz file provided in examples folder. 
+Script `installation-test` also extracts it and compares it with 
+result.profbval. If you want to check that everything goes as expected, 
+you can unzip that file and compare it with the result of above profbval call.
+
+Other notes 
+───────────
+This call is also valid:
+
+  profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp oo,o0,o1,o2,o3,o4,o5,o6,osn,osn2 9 -1,0,1,2,3,4,5,6,snap,snapfun
+
+Providing 6 positional parameters is always mandatory (there is also 1 
+additional parameter).
+
+PROFbval can save results to different locations (not to current folder - works 
+well with relative and absolute paths), however, it fails when directory of 
+interest doesn't exist.
+
+More details on parameters and output formats are available in the package's man 
+page (run `man profbval`) or can be found in associated articles [1]. 
+
+Man page describes how to generate HSSP input file. If you wonder, how to get rdbProf 
+file, Rost Lab's PROFbval Wiki page [2] suggests following procedure:
+  
+  Generating an rdbProf file requires generating an HSSP input file. The HSSP 
+  input file is used as input to the prof program.
+    
+    prof <filtered_hssp_file> both numresMin=17 nresPerLineAli=60 riSubSec=4 riSubAcc=3 fileRdb=<rdbProf_file>
+
+Mentioned `prof` program is a part of `profphd` package listed in this package's
+recommendations list.
+ 
+References:
+
+[1]: PROFbval-related articles, mentioned in package's debian/upstream/metadata
+    http://www.ncbi.nlm.nih.gov/pubmed/16455751
+    http://www.ncbi.nlm.nih.gov/pubmed/16080156
+[2]: Rost Lab's PROFbval Wiki page
+    https://rostlab.org/owiki/index.php/PROFbval

Modified: trunk/packages/profbval/trunk/debian/changelog
===================================================================
--- trunk/packages/profbval/trunk/debian/changelog	2016-06-09 14:33:26 UTC (rev 22120)
+++ trunk/packages/profbval/trunk/debian/changelog	2016-06-09 16:53:38 UTC (rev 22121)
@@ -5,6 +5,7 @@
     corresponding PMID article link
   * add simple testsuite
   * cme fix dpkg-control
+  * added d/README.test + d/docs, improved installation-test
 
  -- Tatiana Malygina <merlettaia at gmail.com>  Wed, 08 Jun 2016 17:41:47 +0000
 

Added: trunk/packages/profbval/trunk/debian/docs
===================================================================
--- trunk/packages/profbval/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/profbval/trunk/debian/docs	2016-06-09 16:53:38 UTC (rev 22121)
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/installation-test

Modified: trunk/packages/profbval/trunk/debian/tests/installation-test
===================================================================
--- trunk/packages/profbval/trunk/debian/tests/installation-test	2016-06-09 14:33:26 UTC (rev 22120)
+++ trunk/packages/profbval/trunk/debian/tests/installation-test	2016-06-09 16:53:38 UTC (rev 22121)
@@ -21,5 +21,8 @@
 done
 
 # call example from man:
-profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp cad23.profbval 9 6
-[ -s cad23.profbval ]
+profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp result.profbval 9 6
+[ -s result.profbval ]
+#there is also gzipped output from package's authors, we can compare result 
+#from profbval call with that sample output - it must be the same
+cmp --silent result.profbval cad23.profbval