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| author | Pjotr Prins | 2018-02-10 07:53:53 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2018-02-10 07:53:53 +0000 |
| commit | 97ccc478543a7bb08fe0cf178e320dd5811d8bfa (patch) | |
| tree | 65c3610e421eea8615c377d922ad63d6cd258bde | |
| parent | 4ae2d548127eeeaa7cec0baf1b788005b5e8e51d (diff) | |
| download | genenetwork2-97ccc478543a7bb08fe0cf178e320dd5811d8bfa.tar.gz | |
Check for bimbam path and bail out if it is missing
| -rwxr-xr-x | bin/genenetwork2 | 1 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 4 |
3 files changed, 2 insertions, 4 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index f64576d5..7148c022 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -45,6 +45,7 @@ SCRIPT=$(realpath "$0") echo SCRIPT=$SCRIPT +echo GN2_PROFILE=$GN2_PROFILE GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1ef2bc26..1e66e957 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) +assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 57f97a81..e3fcd7c7 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -278,8 +278,4 @@ if os.environ.get('WQFLASK_OVERRIDES'): logger.debug(OVERRIDES) # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -# assert_dir(get_setting("JS_BIODALLIANCE")) -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") -# assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") |