Author: christophgil-guest Date: 2012-05-28 14:41:13 +0000 (Mon, 28 May 2012) New Revision: 11032
Modified: trunk/packages/strap/trunk/debian/bin/strap trunk/packages/strap/trunk/debian/strap.1 trunk/packages/strap/trunk/debian/strap.manpages Log: Modified: trunk/packages/strap/trunk/debian/bin/strap =================================================================== --- trunk/packages/strap/trunk/debian/bin/strap 2012-05-28 02:07:14 UTC (rev 11031) +++ trunk/packages/strap/trunk/debian/bin/strap 2012-05-28 14:41:13 UTC (rev 11032) @@ -19,15 +19,16 @@ -echo The maximum heap size option is $xmx. To change, -echo add a program line option like -Xmx500M which means a heap size of 500 Megabytes. +echo The maximum heap size option is $xmx. +echo To change, add a program line option like -Xmx500M +echo which would set heap size to 500 Megabytes. echo -EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -probeWebProxy -stdout -askUpload $*" - +EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload $*" + echo echo $EXEC echo -exec $EXEC +$EXEC Modified: trunk/packages/strap/trunk/debian/strap.1 =================================================================== --- trunk/packages/strap/trunk/debian/strap.1 2012-05-28 02:07:14 UTC (rev 11031) +++ trunk/packages/strap/trunk/debian/strap.1 2012-05-28 14:41:13 UTC (rev 11032) @@ -128,10 +128,6 @@ -script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *" -\fB\-showScriptText\fR - - Displays the script defined with the -script option. - \fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR Only needed for DAS servers that are @@ -156,6 +152,14 @@ Example: -v3d=jmol or -v3d=pymol or -v3d=astex +\fB\-aligner2\fR=\fIJavaClass\fR + +Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start. +Default value is PairAlignerNeoBioPROXY. + +Example: -aligner2=MultipleAlignerClustalW + + \fB\-log3d\fR All 3D-commands which are sent to 3D-protein viewers are printed to stdout. @@ -231,6 +235,17 @@ to remote servers. The user might not want unpublished sequences to be sent to servers. +\fB\-askExec\fR[=t/f] The user is asked when an external program is +executed. Executing native programs might be regarded as security +risk. There is a positive and a negative list which can be edited in +the menu "Security" of the Preferences-menu. + +\fB\-allowFileModification\fR According to the default policy, files +are only modified, created or deleted if they reside in the project +directory or if the file path contains "StrapAlign". This is to +prevent files to be lost. With this option file modification control +is deactivated. + .SH PROJECT DIRECTORY The project directory holds information for gaps, 3D-transformations, Modified: trunk/packages/strap/trunk/debian/strap.manpages =================================================================== --- trunk/packages/strap/trunk/debian/strap.manpages 2012-05-28 02:07:14 UTC (rev 11031) +++ trunk/packages/strap/trunk/debian/strap.manpages 2012-05-28 14:41:13 UTC (rev 11032) @@ -1 +1 @@ -debian/*1 +debian/strap.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
