Andreas Tille pushed to branch master at Debian Med / primer3
Commits:
388a4614 by Andreas Tille at 2018-02-21T09:19:51+01:00
Adapt patches
- - - - -
3993096e by Andreas Tille at 2018-02-21T09:21:18+01:00
Standards-Version: 4.1.3
- - - - -
804a5d02 by Andreas Tille at 2018-02-21T09:21:39+01:00
debhelper 11
- - - - -
4afea24e by Andreas Tille at 2018-02-21T09:39:28+01:00
Doc was moved to src, settings files were moved as well
- - - - -
32549cc5 by Andreas Tille at 2018-02-21T09:48:12+01:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/patches/hardening.patch
- debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
- debian/primer3.docs
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,11 @@
-primer3 (2.4.0-1) UNRELEASED; urgency=medium
+primer3 (2.4.0-1) unstable; urgency=medium
* New upstream version
* Secure URI in watch file
+ * Standards-Version: 4.1.3
+ * debhelper 11
- -- Andreas Tille <ti...@debian.org> Wed, 21 Feb 2018 09:01:27 +0100
+ -- Andreas Tille <ti...@debian.org> Wed, 21 Feb 2018 09:21:42 +0100
primer3 (2.3.7-5) unstable; urgency=medium
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,8 +5,8 @@ Uploaders: Steffen Moeller <moel...@debian.org>,
Andreas Tille <ti...@debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.0
+Build-Depends: debhelper (>= 11)
+Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/primer3.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/primer3.git
Homepage: http://primer3.sourceforge.net
=====================================
debian/patches/hardening.patch
=====================================
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -15,7 +15,7 @@ Description: Propagate hardening options
# Note, for profiling, use
# make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
-@@ -163,7 +163,7 @@ $(NTTHAL_EXE): thal_main.o thal.o
+@@ -175,7 +175,7 @@ $(NTTHAL_EXE): thal_main.o thal.o
$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
=====================================
debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
=====================================
--- a/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
+++ b/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
@@ -8,7 +8,7 @@ Description: Configuration in /etc
--- a/src/primer3_boulder_main.c
+++ b/src/primer3_boulder_main.c
-@@ -505,18 +505,18 @@ read_thermodynamic_parameters()
+@@ -539,18 +539,18 @@ read_thermodynamic_parameters()
return;
}
#else
@@ -46,7 +46,7 @@ Description: Configuration in /etc
fprintf(stderr, "Error: thermodynamic approach chosen, but path to
thermodynamic parameters not specified\n");
--- a/src/release_notes.txt
+++ b/src/release_notes.txt
-@@ -218,9 +218,9 @@ defaults. The default is --default_vers
+@@ -272,9 +272,9 @@ defaults. The default is --default_vers
1.5 IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1,
PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location.
This tag specifies the path to the directory that contains all the
@@ -58,26 +58,23 @@ Description: Configuration in /etc
there is only one default location: .\primer3_config\. If the the
parameter files are not in one these locations, be sure to set
PRIMER_THERMODYNAMIC_PARAMETERS_PATH
---- a/primer3_manual.htm
-+++ b/primer3_manual.htm
-@@ -229,9 +229,9 @@ defaults. The default is --default_vers
- 2.5. IMPORTANT: because <a
href="#PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT">PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT</a>=1,
- <a
href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>
must point to the right location.
+--- a/src/primer3_manual.htm
++++ b/src/primer3_manual.htm
+@@ -222,7 +222,7 @@ defaults. The default is --default_vers
This tag specifies the path to the directory that contains all the
--parameter files used by the thermodynamic approach. In Linux, there
-+parameter files used by the thermodynamic approach. In Debian, there
+ parameter files used by the thermodynamic approach. In Linux, there
are two *default* locations that are tested if this tag is not
-defined: ./primer3_config/ and /opt/primer3_config/. For Windows,
+defined: ./primer3_config/ and /etc/primer3_config/. For Windows,
there is only one default location: .\primer3_config\. If the the
parameter files are not in one these locations, be sure to set
<a
href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>.<br>
-@@ -2452,7 +2452,7 @@ the propensity of oligos to anneal to un
+@@ -2082,7 +2082,7 @@ the propensity of oligos to anneal to un
<p>This tag specifies the path to the directory that contains all the
parameter files used by the thermodynamic approach. In Linux, there are two
- default locations that are tested if this tag is not defined:
+ default locations that are tested if this tag is not defined:
-<i>./primer3_config/</i> and <i>/opt/primer3_config/</i>.
+<i>./primer3_config/</i> and <i>/etc/primer3_config/</i>.
For Windows, there is only one default location: <i>.\primer3_config\</i>.</p>
-
-
+ <h3><a name="PRIMER_MAX_SELF_ANY">PRIMER_MAX_SELF_ANY (decimal, 9999.99;
default 8.00)</a></h3>
+ <p>PRIMER_MAX_SELF_ANY describes the tendency of a primer to bind to
=====================================
debian/primer3.docs
=====================================
--- a/debian/primer3.docs
+++ b/debian/primer3.docs
@@ -1,3 +1,3 @@
-primer3_manual.htm
+src/primer3_manual.htm
src/release_notes.txt
debian/README.test
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -23,7 +23,7 @@ override_dh_installexamples:
mkdir -p $(sampledir)/src;
cp -aR ./test/* $(sampledir)/test;
cp -aR ./src/humrep_and_simple.txt $(sampledir)/src;
- cp primer*.txt $(sampledir)/;
+ cp -a settings_files/primer*.txt $(sampledir)/;
chmod -x $(sampledir)/test/thal*;
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#'
$(sampledir)/test/long_seq_tm_test.pl ;
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#'
$(sampledir)/test/vgrep.pl ;
View it on GitLab:
https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc
---
View it on GitLab:
https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc
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