Package: primer3 / 2.3.6-1

primer_thermodynamic_parameters_path_2_etc.patch Patch series | download
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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
@@ -505,18 +505,18 @@ read_thermodynamic_parameters()
       return;
     }
 #else
-    /* in linux, check for ./primer3_config and /opt/primer3_config */
+    /* in Debian, check for ./primer3_config and /etc/primer3_config */
     struct stat st;
     if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
       thermodynamic_params_path =
 	(char*) malloc(strlen("./primer3_config/") * sizeof(char) + 1);
       if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
       strcpy(thermodynamic_params_path, "./primer3_config/");
-    } else if ((stat("/opt/primer3_config", &st) == 0)  && S_ISDIR(st.st_mode)) {
+    } else if ((stat("/etc/primer3_config", &st) == 0)  && S_ISDIR(st.st_mode)) {
       thermodynamic_params_path =
-	(char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1);
+	(char*) malloc(strlen("/etc/primer3_config/") * sizeof(char) + 1);
       if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
-      strcpy(thermodynamic_params_path, "/opt/primer3_config/");
+      strcpy(thermodynamic_params_path, "/etc/primer3_config/");
     } else {
       /* no default directory found */
       return;
--- a/src/thal_main.c
+++ b/src/thal_main.c
@@ -303,8 +303,8 @@ if(a.debug == 0) {
 #else 
      if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
        tmp_ret = get_thermodynamic_values("./primer3_config/", &o);
-     } else if ((stat("/opt/primer3_config", &st) == 0)  && S_ISDIR(st.st_mode)) {
-       tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o);
+     } else if ((stat("/etc/primer3_config", &st) == 0)  && S_ISDIR(st.st_mode)) {
+       tmp_ret = get_thermodynamic_values("/etc/primer3_config/", &o);
      } else {
        /* no default directory found, error */
        fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");
--- a/src/release_notes.txt
+++ b/src/release_notes.txt
@@ -151,9 +151,9 @@ 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/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.
 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
 <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>.<br>
@@ -2452,7 +2452,7 @@ 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: 
-<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>