Author: tille Date: 2009-04-30 20:57:26 +0000 (Thu, 30 Apr 2009) New Revision: 3339
Added: trunk/packages/plink/trunk/debian/NEWS.Debian trunk/packages/plink/trunk/debian/p-link.1 Removed: trunk/packages/plink/trunk/debian/patches/ trunk/packages/plink/trunk/debian/snplink.1 Modified: trunk/packages/plink/trunk/debian/README.Debian trunk/packages/plink/trunk/debian/README.source trunk/packages/plink/trunk/debian/changelog trunk/packages/plink/trunk/debian/control trunk/packages/plink/trunk/debian/plink.links trunk/packages/plink/trunk/debian/rules Log: Adapt to new upstream version which has applied Debian patches; the rename of plink is not done to snplink but to p-link Added: trunk/packages/plink/trunk/debian/NEWS.Debian =================================================================== --- trunk/packages/plink/trunk/debian/NEWS.Debian (rev 0) +++ trunk/packages/plink/trunk/debian/NEWS.Debian 2009-04-30 20:57:26 UTC (rev 3339) @@ -0,0 +1,26 @@ +Name conflict with plink from ssh clone putty +============================================= + +We are facing a name clash in the Free Software universe and we have +to circumvent. + + 1. The plink executable will be copied to + /usr/lib/plink/plink + 2. A symlink + /usr/bin/p-link + 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/README.Debian =================================================================== --- trunk/packages/plink/trunk/debian/README.Debian 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/README.Debian 2009-04-30 20:57:26 UTC (rev 3339) @@ -25,7 +25,7 @@ 1. The plink executable will be copied to /usr/lib/plink/plink 2. A symlink - /usr/bin/snplink + /usr/bin/p-link points to this location. So if you want to use plink with its original name just do the Modified: trunk/packages/plink/trunk/debian/README.source =================================================================== --- trunk/packages/plink/trunk/debian/README.source 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/README.source 2009-04-30 20:57:26 UTC (rev 3339) @@ -1,6 +1,4 @@ -Mark of the ftpmasters has requested the gPLINK.jar to disappear. This -seems like a rightous request of his since that file is produced by an -independent package that still waits to be packaged. +Mark of the ftpmasters has requested the gPLINK.jar to disappear. This removal will be automatically done if you are using the debian/get-orig-source Modified: trunk/packages/plink/trunk/debian/changelog =================================================================== --- trunk/packages/plink/trunk/debian/changelog 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/changelog 2009-04-30 20:57:26 UTC (rev 3339) @@ -1,4 +1,4 @@ -plink (1.05-1) unstable; urgency=low +plink (1.06-1) unstable; urgency=low * New upstream version * debian/get-orig-source @@ -6,10 +6,12 @@ * 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 + /usr/bin/p-link to this location; renamed manpage accordingly Added explicit hint in README.Debian how to proceed if you need the original name. Closes: #503367 + * debian/patches/* - removed because applied upstream + * removed quilt dependency which is not needed any more -- Andreas Tille <[email protected]> Tue, 31 Mar 2009 22:28:25 +0200 Modified: trunk/packages/plink/trunk/debian/control =================================================================== --- trunk/packages/plink/trunk/debian/control 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/control 2009-04-30 20:57:26 UTC (rev 3339) @@ -4,7 +4,7 @@ Maintainer: Debian-Med Packaging Team <[email protected]> Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 5), quilt +Build-Depends: debhelper (>= 5) Standards-Version: 3.8.1 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/ @@ -25,3 +25,7 @@ association with the disease phenotypes. The joint investigation of copy number variations is supported. A variety of statistical tests have been implemented. + . + Please note: The executable was renamed to p-link + because of a name clash. Please read more about this + in /usr/share/doc/README.Debian. Added: trunk/packages/plink/trunk/debian/p-link.1 =================================================================== --- trunk/packages/plink/trunk/debian/p-link.1 (rev 0) +++ trunk/packages/plink/trunk/debian/p-link.1 2009-04-30 20:57:26 UTC (rev 3339) @@ -0,0 +1,29 @@ +.\" Hey, EMACS: -*- nroff -*- +.TH P-LINK 1 "April 8, 2008" +.SH NAME +p-link \- whole genome SNP analysis +.SH SYNOPSIS +.B p-link --help +.SH DESCRIPTION + +This binary was renamed from plink to p-link 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. + +P-link 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 p-link 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.links =================================================================== --- trunk/packages/plink/trunk/debian/plink.links 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/plink.links 2009-04-30 20:57:26 UTC (rev 3339) @@ -1 +1 @@ -usr/lib/plink/plink usr/bin/snplink +usr/lib/plink/plink usr/bin/p-link Modified: trunk/packages/plink/trunk/debian/rules =================================================================== --- trunk/packages/plink/trunk/debian/rules 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/rules 2009-04-30 20:57:26 UTC (rev 3339) @@ -1,7 +1,7 @@ #!/usr/bin/make -f # -*- makefile -*- -include /usr/share/quilt/quilt.make +# include /usr/share/quilt/quilt.make build: patch build-stamp build-stamp: Deleted: trunk/packages/plink/trunk/debian/snplink.1 =================================================================== --- trunk/packages/plink/trunk/debian/snplink.1 2009-04-30 20:28:39 UTC (rev 3338) +++ trunk/packages/plink/trunk/debian/snplink.1 2009-04-30 20:57:26 UTC (rev 3339) @@ -1,29 +0,0 @@ -.\" 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
