[med-svn] [paml] 02/03: Revert patch to seek CTL files in /etc to not derive from previous behaviour. Instead copy CTL files from /etc/paml if there is no local one
Andreas Tille
tille at debian.org
Wed May 4 08:06:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository paml.
commit 49c675285c271baa27b44bc7a73ba01c69b1a67c
Author: Andreas Tille <tille at debian.org>
Date: Wed May 4 10:02:42 2016 +0200
Revert patch to seek CTL files in /etc to not derive from previous behaviour. Instead copy CTL files from /etc/paml if there is no local one
---
debian/bin/baseml | 11 ++++
debian/bin/basemlg | 1 +
debian/bin/codeml | 1 +
debian/bin/mcmctree | 1 +
debian/bin/pamp | 1 +
debian/bin/yn00 | 1 +
debian/changelog | 4 +-
debian/paml.install | 6 +++
debian/paml.links | 8 +--
debian/patches/ctl_files_in_etc.patch | 96 -----------------------------------
debian/patches/series | 1 -
debian/rules | 1 +
12 files changed, 27 insertions(+), 105 deletions(-)
diff --git a/debian/bin/baseml b/debian/bin/baseml
new file mode 100755
index 0000000..d2b8c2b
--- /dev/null
+++ b/debian/bin/baseml
@@ -0,0 +1,11 @@
+#!/bin/sh -e
+BIN=`basename $0`
+if [ "$BIN" = "basemlg" ] ; then
+ CTL=baseml.ctl
+else
+ CTL="$BIN".ctl
+fi
+if [ ! -f $CTL ] ; then
+ cp -a /etc/paml/$CTL .
+fi
+/usr/lib/paml/bin/$BIN $@
diff --git a/debian/bin/basemlg b/debian/bin/basemlg
new file mode 120000
index 0000000..c35244d
--- /dev/null
+++ b/debian/bin/basemlg
@@ -0,0 +1 @@
+baseml
\ No newline at end of file
diff --git a/debian/bin/codeml b/debian/bin/codeml
new file mode 120000
index 0000000..c35244d
--- /dev/null
+++ b/debian/bin/codeml
@@ -0,0 +1 @@
+baseml
\ No newline at end of file
diff --git a/debian/bin/mcmctree b/debian/bin/mcmctree
new file mode 120000
index 0000000..c35244d
--- /dev/null
+++ b/debian/bin/mcmctree
@@ -0,0 +1 @@
+baseml
\ No newline at end of file
diff --git a/debian/bin/pamp b/debian/bin/pamp
new file mode 120000
index 0000000..c35244d
--- /dev/null
+++ b/debian/bin/pamp
@@ -0,0 +1 @@
+baseml
\ No newline at end of file
diff --git a/debian/bin/yn00 b/debian/bin/yn00
new file mode 120000
index 0000000..c35244d
--- /dev/null
+++ b/debian/bin/yn00
@@ -0,0 +1 @@
+baseml
\ No newline at end of file
diff --git a/debian/changelog b/debian/changelog
index 64804f0..3264966 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-paml (4.91+dfsg-1) UNRELEASED; urgency=medium
+paml (4.91+dfsg-1) unstable; urgency=medium
* New upstream version
* Author confirmed GPL license at
@@ -12,7 +12,7 @@ paml (4.91+dfsg-1) UNRELEASED; urgency=medium
* *.ctl files are symlinked to /etc/paml and found properly by the
according code
- -- Andreas Tille <tille at debian.org> Mon, 02 May 2016 15:37:17 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 03 May 2016 14:24:12 +0200
paml (4.8+dfsg-1) unstable; urgency=medium
diff --git a/debian/paml.install b/debian/paml.install
index a5cd29b..a4149a7 100644
--- a/debian/paml.install
+++ b/debian/paml.install
@@ -6,6 +6,12 @@ src/evolver usr/lib/paml/bin
src/mcmctree usr/lib/paml/bin
src/pamp usr/lib/paml/bin
src/yn00 usr/lib/paml/bin
+debian/bin/baseml usr/lib/debian-med/bin
+debian/bin/basemlg usr/lib/debian-med/bin
+debian/bin/codeml usr/lib/debian-med/bin
+debian/bin/mcmctree usr/lib/debian-med/bin
+debian/bin/pamp usr/lib/debian-med/bin
+debian/bin/yn00 usr/lib/debian-med/bin
*.aa usr/lib/paml/data
*.ctl usr/lib/paml/data
*.dat usr/lib/paml/data
diff --git a/debian/paml.links b/debian/paml.links
index 8985fd8..efb8c86 100644
--- a/debian/paml.links
+++ b/debian/paml.links
@@ -1,17 +1,13 @@
# provide full set of tools in Debian Med scope as well
-usr/lib/paml/bin/baseml usr/lib/debian-med/bin/baseml
-usr/lib/paml/bin/basemlg usr/lib/debian-med/bin/basemlg
usr/lib/paml/bin/chi2 usr/lib/debian-med/bin/chi2
-usr/lib/paml/bin/codeml usr/lib/debian-med/bin/codeml
-usr/lib/paml/bin/evolver usr/lib/debian-med/bin/evolver
-usr/lib/paml/bin/pamp usr/lib/debian-med/bin/pamp
-usr/lib/paml/bin/yn00 usr/lib/debian-med/bin/yn00
+usr/lib/paml/bin/evolver usr/lib/debian-med/bin/evolver
# provide renamed evolver in usr/bin
usr/lib/debian-med/bin/baseml usr/bin/baseml
usr/lib/debian-med/bin/basemlg usr/bin/basemlg
usr/lib/debian-med/bin/chi2 usr/bin/chi2
usr/lib/debian-med/bin/codeml usr/bin/codeml
usr/lib/debian-med/bin/evolver usr/bin/paml-evolver
+usr/lib/debian-med/bin/mcmctree usr/bin/mcmctree
usr/lib/debian-med/bin/pamp usr/bin/pamp
usr/lib/debian-med/bin/yn00 usr/bin/yn00
diff --git a/debian/patches/ctl_files_in_etc.patch b/debian/patches/ctl_files_in_etc.patch
deleted file mode 100644
index 6398d79..0000000
--- a/debian/patches/ctl_files_in_etc.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-Description: Debian package symlinks *.ctl files to /etc/paml. This patch
- ensures that the code is seeking at the same location.
-Author: Andreas Tille <tille at debian.org>
-Last-Update Mon, 02 May 2016 15:37:17 +0200
-
---- a/src/baseml.c
-+++ b/src/baseml.c
-@@ -132,7 +132,7 @@ int main (int argc, char *argv[])
- {
- FILE *fout, *fseq=NULL, *fpair[6];
- char pairfs[1][32]={"2base.t"};
-- char rstf[512]="rst", ctlf[512]="baseml.ctl", timestr[64];
-+ char rstf[512]="rst", ctlf[512]="/etc/paml/baseml.ctl", timestr[64];
- char *Mgenestr[]={"diff. rate", "separate data", "diff. rate & pi",
- "diff. rate & kappa", "diff. rate & pi & kappa"};
- int getdistance=1, i, idata;
---- a/src/basemlg.c
-+++ b/src/basemlg.c
-@@ -83,7 +83,7 @@ int main (int argc, char *argv[])
- {
- FILE *fout, *fseq=NULL, *fpair[6];
- char pairfs[1][32]={"2base.t"};
-- char ctlf[96]="baseml.ctl";
-+ char ctlf[512]="/etc/paml/baseml.ctl";
- double space[50000];
-
- noisy=2; com.cleandata=1; /* works with clean data only */
-@@ -810,7 +810,7 @@ int GetOptions (char *ctlf)
- if (com.alpha<=0) error2("init alpha..");
- if (com.alpha==0 || com.Malpha || com.rho>0 || com.nhomo>0 || com.nparK>0
- || com.model>HKY85)
-- error2 ("\noptions in file baseml.ctl inappropriate.. giving up..");
-+ error2 ("\noptions in file /etc/paml/baseml.ctl inappropriate.. giving up..");
- if (com.model==JC69 || com.model==F81) { com.fix_kappa=1; com.kappa=1; }
- if(com.cleandata==0) {
- puts("cleandata set to 1, with ambiguity data removed. ");
---- a/src/codeml.c
-+++ b/src/codeml.c
-@@ -242,7 +242,7 @@ int main (int argc, char *argv[])
- {
- FILE *fseq=NULL, *fpair[6];
- char pairfs[6][32]={"2NG.dS","2NG.dN","2NG.t", "2ML.dS","2ML.dN","2ML.t"};
-- char ctlf[96]="codeml.ctl", *pmodel, timestr[64];
-+ char ctlf[512]="/etc/paml/codeml.ctl", *pmodel, timestr[64];
- char *seqtypestr[3]={"CODONML", "AAML", "CODON2AAML"};
- char *Mgenestr[]={"diff. rate", "separate data", "diff. rate & pi",
- "diff. rate & k&w", "diff. rate & pi & k&w"};
-@@ -1448,7 +1448,7 @@ void DetailOutput (FILE *fout, double x[
-
- void ReadNSsitesModels(char *line)
- {
--/* This reads the line NSsites = 0 1 2 3 7 8 in codeml.ctl.
-+/* This reads the line NSsites = 0 1 2 3 7 8 in /etc/paml/codeml.ctl.
- */
- char *pline;
- int pop_digit;
---- a/src/mcmctree.c
-+++ b/src/mcmctree.c
-@@ -191,7 +191,7 @@ char *Btransform[]={"", "square root", "
-
- int main (int argc, char *argv[])
- {
-- char ctlf[512] = "mcmctree.ctl";
-+ char ctlf[512] = "/etc/paml/mcmctree.ctl";
- int i, j, k=4;
- FILE *fout;
-
---- a/src/pamp.c
-+++ b/src/pamp.c
-@@ -1,5 +1,5 @@
- /* PAMP.c, Copyright, Ziheng Yang, April 1995.
-- Specify the sequence type in the file pamp.ctl. Results go into mp.
-+ Specify the sequence type in the file /etc/paml/pamp.ctl. Results go into mp.
-
- gcc -o pamp pamp.c tools.o
- pamp <ControlFileName>
-@@ -68,7 +68,7 @@ int LASTROUND=0; /* no use for this */
- int main (int argc, char *argv[])
- {
- FILE *ftree, *fout, *fseq;
-- char ctlf[32]="pamp.ctl";
-+ char ctlf[512]="/etc/paml/pamp.ctl";
- char *Seqstr[]={"nucleotide", "", "amino-acid", "Binary"};
- int itree, ntree, i, j, s3;
- double *space, *Ft;
---- a/src/yn00.c
-+++ b/src/yn00.c
-@@ -74,7 +74,7 @@ int main(int argc, char *argv[])
- {
- char dsf[512]="2YN.dS", dnf[512]="2YN.dN", tf[512]="2YN.t";
- FILE *fout, *fseq, *fds, *fdn, *ft;
-- char ctlf[96]="yn00.ctl", timestr[64];
-+ char ctlf[512]="/etc/paml/yn00.ctl", timestr[64];
- int n=com.ncode, is,js, j, idata, wname=20, sspace;
- double t=0.4, dS=0.1,dN=0.1, S,N, SEdS, SEdN, f3x4[12], *space=NULL;
-
diff --git a/debian/patches/series b/debian/patches/series
index 0727394..8135895 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
fix_format_security.patch
hardening.patch
add_clean_target.patch
-ctl_files_in_etc.patch
diff --git a/debian/rules b/debian/rules
index c413505..72897a4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -27,6 +27,7 @@ override_dh_install:
$${datfile} ; \
done ; \
done
+ sed -i 's?\(aaRatefile = \)\(dat/jones.dat\)?\1$(DATADIR)/\2?' debian/$(DEBPKGNAME)/$(DATADIR)/codeml.ctl
override_dh_link:
dh_link
--
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