Author: christophgil-guest Date: 2012-12-18 22:26:35 +0000 (Tue, 18 Dec 2012) New Revision: 12695
Modified: trunk/packages/strap/trunk/debian/bin/strap_protein_alignment trunk/packages/strap/trunk/debian/strap_protein_alignment.1 Log: Removed soft link for man page file Modified: trunk/packages/strap/trunk/debian/bin/strap_protein_alignment =================================================================== --- trunk/packages/strap/trunk/debian/bin/strap_protein_alignment 2012-12-18 22:25:36 UTC (rev 12694) +++ trunk/packages/strap/trunk/debian/bin/strap_protein_alignment 2012-12-18 22:26:35 UTC (rev 12695) @@ -4,10 +4,7 @@ echo -S3D= -if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi +/bin/sh /usr/bin/strap_base -probeWebProxy -stdout $* -/bin/sh /usr/bin/strap_base $S3D -a3d=mustang -aligner2=kalign -v3d=pymol -probeWebProxy -stdout -askUpload $* - \ No newline at end of file Modified: trunk/packages/strap/trunk/debian/strap_protein_alignment.1 =================================================================== --- trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2012-12-18 22:25:36 UTC (rev 12694) +++ trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2012-12-18 22:26:35 UTC (rev 12695) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH Strap 1 "October 2011" .SH NAME @@ -132,8 +132,13 @@ -script="open_3D viewName, *" would display all proteins with 3D-coordinates three-dimensionally (See -v3d=). Scripts consisting of more than one line should be -stored in a file and the file path or URL should be given. +stored in a file and the file path or URL should be given. +If scripts are run on a server which allows many instances simultaneously, +consider to use a database backend instead of the file based cache for computed results +(See http://www.bioinformatics.org/strap/cache.html) + + Example: -script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *" @@ -195,16 +200,11 @@ \fB\-noCache\fR - Do not use cached results of previous +Do not use cached results of previous computations. This setting can be changed in the graphical user interface with a check-box. +Also see http://www.bioinformatics.org/strap/cache.html. -This setting influences the result of searches in growing -databases. For example consider the similarity search method -Blast. With the cache turned on, Strap would present a previously -computed Blast result even though new sequences might have been -published since last run. - \fB\-keepFiles\fR Do not delete temp-files after the session. This is only important for @@ -265,6 +265,23 @@ is deactivated. +.SH Parameters for the Java virtual machine + +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + .SH ALIGNMENT FILE GENERATION With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
