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-rw-r--r--doc/README.org11
-rw-r--r--wqflask/utility/tools.py1
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py4
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py4
4 files changed, 11 insertions, 9 deletions
diff --git a/doc/README.org b/doc/README.org
index ee54f781..3b96717f 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -134,12 +134,17 @@ configuration.
** Run your own copy of GN2
-At some point you may want to fix the source code. Clone the GN2
-repository from https://github.com/genenetwork/genenetwork2_diet
+At some point you may want to fix the source code. Assuming you have
+Guix and Genenetwork2 installed (as described above) clone the GN2
+repository from https://github.com/genenetwork/genenetwork2_diet
+
+Copy the paths into your terminal from (mainly so PYTHON_PATH and
+R_LIBS_SITE are set)
+
+: guix package --search-paths
Inside the repository:
-: git clone
: cd genenetwork2_diet
: ./bin/genenetwork2
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9405a9c6..dd8c4a1e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -5,7 +5,6 @@ import os
import sys
from wqflask import app
-
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with get_valid_path is a function checking whether the
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index ae426621..8fb086c1 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,9 +1,7 @@
import os
from base import webqtlConfig
-from utility.tools import gemma_command
-
-GEMMA_PATH,GEMMA_COMMAND = gemma_command()
+from utility.tools import GEMMA_COMMAND
def run_gemma(this_dataset, samples, vals):
"""Generates p-values for each marker using GEMMA"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 39d7c78a..97949f93 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -1103,5 +1103,5 @@ def get_markers_from_csv(included_markers, p_values, group_name):
return markers
- if __name__ == '__main__':
- import cPickle as pickle
+if __name__ == '__main__':
+ import cPickle as pickle