Author: tille Date: 2009-04-01 12:33:15 +0000 (Wed, 01 Apr 2009) New Revision: 3261
Added: trunk/packages/plink/trunk/debian/plink.links trunk/packages/plink/trunk/debian/snplink.1 Removed: trunk/packages/plink/trunk/debian/plink.1 Modified: trunk/packages/plink/trunk/debian/README.Debian trunk/packages/plink/trunk/debian/changelog trunk/packages/plink/trunk/debian/manpages trunk/packages/plink/trunk/debian/plink.install Log: Try to solve the naming problem (#503367) Modified: trunk/packages/plink/trunk/debian/README.Debian =================================================================== --- trunk/packages/plink/trunk/debian/README.Debian 2009-04-01 12:13:30 UTC (rev 3260) +++ trunk/packages/plink/trunk/debian/README.Debian 2009-04-01 12:33:15 UTC (rev 3261) @@ -10,4 +10,35 @@ Debian-Med.alioth.debian.org community has brought ot Debian, e.g. r-cran-qtl and general packages for bioinformatics research. - -- Steffen Moeller <[email protected]> Tue, 15 Jul 2008 00:13:15 +0200 + +Name conflict with plink from ssh clone putty +============================================= + +At http://bugs.debian.org/503367 you can read the full discussion +about a name clash between one component of the frequently used +ssh software putty and plink. The short story is: We are facing a +name clash in the Free Software universe and we have to circumvent +this somehow. Following the arguing in the bug discussion the +plink package has to do the name change. So we found the following +solution: + + 1. The plink executable will be copied to + /usr/lib/plink/plink + 2. A symlink + /usr/bin/snplink + points to this location. + +So if you want to use plink with its original name just do the +following: Set the PATH variable like + + export PATH="/usr/lib/plink:$PATH" + +or alternatively set a symlink into a directory which is normally in +your PATH anyway like + + ln -s /usr/lib/plink/plink /usr/local/bin/plink + +if /usr/local/bin is in your PATH. This makes sure that scripts you +are using will find the correct plink executable. + + -- Andreas Tille <[email protected]> Tue, 31 Mar 2009 22:28:25 +0200 Modified: trunk/packages/plink/trunk/debian/changelog =================================================================== --- trunk/packages/plink/trunk/debian/changelog 2009-04-01 12:13:30 UTC (rev 3260) +++ trunk/packages/plink/trunk/debian/changelog 2009-04-01 12:33:15 UTC (rev 3261) @@ -5,6 +5,11 @@ * Standards-Version: 3.8.1 (no changes needed) * Applied gcc4.3 patch from gentoo (Thanks to Andrey Kislyuk <[email protected]>) + * Moved plink executable to /usr/lib/plink and symlinked + /usr/bin/snplink to this location; renamed manpage accordingly + Added explicit hint in README.Debian how to proceed if you + need the original name. + Closes: #503367 -- Andreas Tille <[email protected]> Tue, 31 Mar 2009 22:28:25 +0200 Modified: trunk/packages/plink/trunk/debian/manpages =================================================================== --- trunk/packages/plink/trunk/debian/manpages 2009-04-01 12:13:30 UTC (rev 3260) +++ trunk/packages/plink/trunk/debian/manpages 2009-04-01 12:33:15 UTC (rev 3261) @@ -1 +1 @@ -debian/plink.1 +debian/*.1 Deleted: trunk/packages/plink/trunk/debian/plink.1 =================================================================== --- trunk/packages/plink/trunk/debian/plink.1 2009-04-01 12:13:30 UTC (rev 3260) +++ trunk/packages/plink/trunk/debian/plink.1 2009-04-01 12:33:15 UTC (rev 3261) @@ -1,25 +0,0 @@ -.\" Hey, EMACS: -*- nroff -*- -.TH PLINK 1 "April 8, 2008" -.SH NAME -plink \- whole genome SNP analysis -.SH SYNOPSIS -.B plink --help -.SH DESCRIPTION - -plink works on SNP datasets that have already been pre-analysed for -their reliability and their calling to AA, BB or AB. It finds associations -with a disease of single SNPs or pairs, determines haplotype blocks or -retrieves information on SNPs from an online repository. - -This manual page must be insufficient. Please use the help option for a -quick reminder of the options of plink or turn to its home page with -the online documentation or the downloadable manual. - -.SH SEE ALSO -.BR http://pngu.mgh.harvard.edu/~purcell/plink - -.SH AUTHOR -plink was written by Shaun Purcell <[email protected]> -.PP -This manual page was written by Steffen Moeller <[email protected]>, -for the Debian project (but may be used by others). Modified: trunk/packages/plink/trunk/debian/plink.install =================================================================== --- trunk/packages/plink/trunk/debian/plink.install 2009-04-01 12:13:30 UTC (rev 3260) +++ trunk/packages/plink/trunk/debian/plink.install 2009-04-01 12:33:15 UTC (rev 3261) @@ -1 +1 @@ -plink usr/bin +plink usr/lib/plink Added: trunk/packages/plink/trunk/debian/plink.links =================================================================== --- trunk/packages/plink/trunk/debian/plink.links (rev 0) +++ trunk/packages/plink/trunk/debian/plink.links 2009-04-01 12:33:15 UTC (rev 3261) @@ -0,0 +1 @@ +usr/lib/plink/plink usr/bin/snplink Copied: trunk/packages/plink/trunk/debian/snplink.1 (from rev 3242, trunk/packages/plink/trunk/debian/plink.1) =================================================================== --- trunk/packages/plink/trunk/debian/snplink.1 (rev 0) +++ trunk/packages/plink/trunk/debian/snplink.1 2009-04-01 12:33:15 UTC (rev 3261) @@ -0,0 +1,29 @@ +.\" Hey, EMACS: -*- nroff -*- +.TH SNPLINK 1 "April 8, 2008" +.SH NAME +snplink \- whole genome SNP analysis +.SH SYNOPSIS +.B snplink --help +.SH DESCRIPTION + +This binary was renamed from plink to snplink because there is a name clash +between this plink and a part of the ssh clone putty. Please read +/usr/share/doc/plink/README.Debian to learn more about this. + +snplink works on SNP datasets that have already been pre-analysed for +their reliability and their calling to AA, BB or AB. It finds associations +with a disease of single SNPs or pairs, determines haplotype blocks or +retrieves information on SNPs from an online repository. + +This manual page must be insufficient. Please use the help option for a +quick reminder of the options of snplink or turn to its home page with +the online documentation or the downloadable manual. + +.SH SEE ALSO +.BR http://pngu.mgh.harvard.edu/~purcell/plink + +.SH AUTHOR +plink was written by Shaun Purcell <[email protected]> +.PP +This manual page was written by Steffen Moeller <[email protected]>, +for the Debian project (but may be used by others). _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
