[med-svn] r3261 - trunk/packages/plink/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Wed Apr 1 12:33:16 UTC 2009
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 <moeller at debian.org> 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 <tille at debian.org> 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
<weaver at gentoo.org>)
+ * 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 <tille at debian.org> 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 <plink at chgr.mgh.harvard.edu>
-.PP
-This manual page was written by Steffen Moeller <moeller at debian.org>,
-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 <plink at chgr.mgh.harvard.edu>
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (but may be used by others).
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