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-rwxr-xr-xbin/genenetwork21
-rw-r--r--etc/default_settings.py1
-rw-r--r--wqflask/utility/tools.py12
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"))