Merge pull request #259 from pjotrp/testing

gemma-wrapper: find binary in profile

3 files changed, 10 insertions, 4 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 236d8f63..e07a4e32 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -78,6 +78,7 @@ else
     export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
     export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
+    export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
 fi
 if [ -z $PYTHONPATH ] ; then
     echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 1b609414..c00f6c8f 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -69,3 +69,4 @@ JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
 # PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
 # PLINK_COMMAND = str.strip(os.popen("which plink2").read())
 # GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
+# GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read())
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 867bc5c8..c5685cdd 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -113,6 +113,9 @@ def pylmm_command(guess=None):
 def gemma_command(guess=None):
     return assert_bin(get_setting("GEMMA_COMMAND",guess))
 
+def gemma_wrapper_command(guess=None):
+    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
+
 def plink_command(guess=None):
     return assert_bin(get_setting("PLINK_COMMAND",guess))
 
@@ -240,10 +243,11 @@ JS_GUIX_PATH       = get_setting('JS_GUIX_PATH')
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
-PYLMM_COMMAND      = pylmm_command()
-GEMMA_COMMAND      = gemma_command()
-PLINK_COMMAND      = plink_command()
-TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
+PYLMM_COMMAND         = pylmm_command()
+GEMMA_COMMAND         = gemma_command()
+GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
+PLINK_COMMAND         = plink_command()
+TEMPDIR               = tempdir() # defaults to UNIX TMPDIR
 
 # ---- Handle specific JS modules
 JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))