[med-svn] r18603 - trunk/packages/plink/trunk/debian
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Thu Jan 22 07:10:32 UTC 2015
Author: bob.dybian-guest
Date: 2015-01-22 07:10:31 +0000 (Thu, 22 Jan 2015)
New Revision: 18603
Added:
trunk/packages/plink/trunk/debian/p-link.1
Modified:
trunk/packages/plink/trunk/debian/NEWS.Debian
trunk/packages/plink/trunk/debian/README.Debian
trunk/packages/plink/trunk/debian/changelog
trunk/packages/plink/trunk/debian/plink.install
trunk/packages/plink/trunk/debian/plink.links
trunk/packages/plink/trunk/debian/rules
Log:
Move plink binary to /usr/lib/debian-med/bin/plink
Modified: trunk/packages/plink/trunk/debian/NEWS.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/NEWS.Debian 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/NEWS.Debian 2015-01-22 07:10:31 UTC (rev 18603)
@@ -5,23 +5,31 @@
to circumvent. To summarize, we have:
1. The plink1 executable
- /usr/bin/plink1
- 2. A symbolic link to the plink1 executable
- /usr/bin/p-link
- 3. The plink1.9 executable
- /usr/bin/plink1.9
- 4. The plink2 executable
- /usr/bin/plink2
- 5. The plink executable (from putty)
+ /usr/lib/debian-med/bin/plink
+ 1.1 A symbolic link to the plink1 executable
+ /usr/bin/plink1
+ /usr/bin/p-link
+ /usr/lib/plink/plink
+
+ 2. The plink1.9 executable
+ /usr/lib/debian-med/bin/plink1.9
+ 2.1 A symbolic link to the plink1.9 executable
+ /usr/bin/plink1.9
+
+ 3. The plink2 executable
+ /usr/lib/debian-med/bin/plink2
+ 3.1 A symbolic link to the plink2 executable
+ /usr/bin/plink2
+
+ 4. The plink executable (from putty)
/usr/bin/plink
-So if you want to use plink1 with its original name just set a
-symlink into a directory which is normally in your PATH anyway like
+So if you want to use plink1 with its original name just do the
+following: Set the PATH variable like
- ln -s /usr/bin/plink1 /usr/local/bin/plink
+ export PATH=/usr/lib/debian-med/bin:$PATH
-if /usr/local/bin is in your PATH. This makes sure that scripts you
-are using will find the correct plink executable.
+This makes sure that scripts you are using will find the correct plink executable.
-- Andreas Tille <tille at debian.org> Tue, 31 Mar 2009 22:28:25 +0200
- -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 10 Jan 2015 23:30:46 +0100
+ -- Dylan Aïssi <bob.dybian at gmail.com> Thu, 22 Jan 2015 08:00:59 +0100
Modified: trunk/packages/plink/trunk/debian/README.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/README.Debian 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/README.Debian 2015-01-22 07:10:31 UTC (rev 18603)
@@ -23,23 +23,31 @@
change. To summarize, we have:
1. The plink1 executable
- /usr/bin/plink1
- 2. A symbolic link to the plink1 executable
- /usr/bin/p-link
- 3. The plink1.9 executable
- /usr/bin/plink1.9
- 4. The plink2 executable
- /usr/bin/plink2
- 5. The plink executable (from putty)
+ /usr/lib/debian-med/bin/plink
+ 1.1 A symbolic link to the plink1 executable
+ /usr/bin/plink1
+ /usr/bin/p-link
+ /usr/lib/plink/plink
+
+ 2. The plink1.9 executable
+ /usr/lib/debian-med/bin/plink1.9
+ 2.1 A symbolic link to the plink1.9 executable
+ /usr/bin/plink1.9
+
+ 3. The plink2 executable
+ /usr/lib/debian-med/bin/plink2
+ 3.1 A symbolic link to the plink2 executable
+ /usr/bin/plink2
+
+ 4. The plink executable (from putty)
/usr/bin/plink
-So if you want to use plink1 with its original name just set a
-symlink into a directory which is normally in your PATH anyway like
+So if you want to use plink1 with its original name just do the
+following: Set the PATH variable like
- ln -s /usr/bin/plink1 /usr/local/bin/plink
+ export PATH=/usr/lib/debian-med/bin:$PATH
-if /usr/local/bin is in your PATH. This makes sure that scripts you
-are using will find the correct plink executable.
+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
- -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 10 Jan 2015 23:30:46 +0100
+ -- Dylan Aïssi <bob.dybian at gmail.com> Thu, 22 Jan 2015 08:00:59 +0100
Modified: trunk/packages/plink/trunk/debian/changelog
===================================================================
--- trunk/packages/plink/trunk/debian/changelog 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/changelog 2015-01-22 07:10:31 UTC (rev 18603)
@@ -6,8 +6,8 @@
* debian/watch: Enable '+dfsg' suffix in Debian versions
[ Dylan Aïssi ]
- * Moved plink executable to /usr/bin/plink1 (and symlinked
- /usr/bin/p-link to this location) in order to prepare cohabitation
+ * Moved plink executable to usr/lib/debian-med/bin/plink (and symlinked
+ old locations to this new location) in order to prepare cohabitation
with plink1.9 and plink2; renamed manpage accordingly
Added explicit hint in README.Debian how to proceed if you
need the original name.
@@ -19,7 +19,7 @@
- Repack using uscan
* debian/tests: Add autopkgtest
- -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 10 Jan 2015 23:30:46 +0100
+ -- Dylan Aïssi <bob.dybian at gmail.com> Thu, 22 Jan 2015 08:00:59 +0100
plink (1.07-3) unstable; urgency=low
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 2015-01-22 07:10:31 UTC (rev 18603)
@@ -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 <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 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/plink.install 2015-01-22 07:10:31 UTC (rev 18603)
@@ -1 +1 @@
-plink1 usr/bin
+plink usr/lib/debian-med/bin/
Modified: trunk/packages/plink/trunk/debian/plink.links
===================================================================
--- trunk/packages/plink/trunk/debian/plink.links 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/plink.links 2015-01-22 07:10:31 UTC (rev 18603)
@@ -1 +1,6 @@
-usr/bin/plink1 usr/bin/p-link
+# For compatibility reasons (i.e. scripts written using plink package <= 1.07-3)
+usr/lib/debian-med/bin/plink usr/bin/p-link
+usr/lib/debian-med/bin/plink usr/lib/plink/plink
+
+# To be consistent with the name of new plink 1.9 and 2
+usr/lib/debian-med/bin/plink usr/bin/plink1
Modified: trunk/packages/plink/trunk/debian/rules
===================================================================
--- trunk/packages/plink/trunk/debian/rules 2015-01-20 20:39:08 UTC (rev 18602)
+++ trunk/packages/plink/trunk/debian/rules 2015-01-22 07:10:31 UTC (rev 18603)
@@ -17,16 +17,11 @@
override_dh_auto_clean:
dh_auto_clean
- rm -f plink1
+ rm -f plink
override_dh_auto_build:
$(MAKE) CXXFLAGS='$(CXXFLAGS)' FORCE_DYNAMIC=1
-override_dh_auto_install:
- # Change binary name
- mv $(CURDIR)/plink $(CURDIR)/plink1
- dh_auto_install
-
override_dh_installexamples:
dh_installexamples
chmod 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/*
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