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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
