1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
Author: Andreas Tille <tille@debian.org>
Last-Changed: Thu, 19 Dec 2013 09:58:19 +0100
Bug-Debian: http://bugs.debian.org/702693
Description: Configuration in /etc
Make sure config files will be searched for in /etc/primer3_config/
instead of /opt/primer3_config/
--- a/src/primer3_boulder_main.c
+++ b/src/primer3_boulder_main.c
@@ -538,7 +538,7 @@ static void validate_kmer_lists_path(){
#endif
#if !defined(OS_WIN)
-/* in linux, check for ../kmer_lists and /opt/kmer_lists */
+/* in Debian, check for ../kmer_lists and /usr/share/doc/primer3/examples/kmer_lists */
static void validate_kmer_lists_path(){
if (kmer_lists_path == NULL) {
struct stat st;
@@ -547,11 +547,11 @@ static void validate_kmer_lists_path(){
(char*) malloc(strlen("../kmer_lists/") * sizeof(char) + 1);
if (NULL == kmer_lists_path) exit (-2); /* Out of memory */
strcpy(kmer_lists_path, "../kmer_lists/");
- } else if ((stat("/opt/kmer_lists", &st) == 0) && S_ISDIR(st.st_mode)) {
+ } else if ((stat("/usr/share/doc/primer3/examples/kmer_lists", &st) == 0) && S_ISDIR(st.st_mode)) {
kmer_lists_path =
- (char*) malloc(strlen("/opt/kmer_lists/") * sizeof(char) + 1);
+ (char*) malloc(strlen("/usr/share/doc/primer3/examples/kmer_lists") * sizeof(char) + 1);
if (NULL == kmer_lists_path) exit (-2); /* Out of memory */
- strcpy(kmer_lists_path, "/opt/kmer_lists/");
+ strcpy(kmer_lists_path, "/usr/share/doc/primer3/examples/kmer_lists");
} else {
/* no default directory found */
return;
--- a/src/release_notes.txt
+++ b/src/release_notes.txt
@@ -371,9 +371,9 @@ 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
-parameter files used by the thermodynamic approach. In Linux, there
+parameter files used by the thermodynamic approach. In Debian, 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
PRIMER_THERMODYNAMIC_PARAMETERS_PATH
--- a/src/primer3_manual.htm
+++ b/src/primer3_manual.htm
@@ -280,7 +280,7 @@ 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
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>
@@ -2337,7 +2337,7 @@ for the turn. For html they have to be r
<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:
-<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 id="PRIMER_ANNEALING_TEMP">PRIMER_ANNEALING_TEMP (float; default -10.0)</a></h3>
<p>The annealing temperature (Celsius) used in the PCR reaction. Usually
|
