diff options
| -rwxr-xr-x | bin/genenetwork2 | 1 | ||||
| -rw-r--r-- | etc/default_settings.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 12 |
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")) |