diff options
| -rw-r--r-- | INSTALL.md | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 4 |
2 files changed, 14 insertions, 5 deletions
diff --git a/INSTALL.md b/INSTALL.md index 38d15090..afe22678 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -1,5 +1,10 @@ # INSTALL Genenetwork2 (GN2) +## Use a Docker image + +A Docker image can be generated from +[here](https://github.com/lomereiter/gn2-docker). + ## Fetch GN2 from github Clone the repository (currently ~800Mb) to local @@ -10,12 +15,14 @@ Clone the repository (currently ~800Mb) to local GN2 requires +* python * redis * mysql ## Required python modules -Install the following python modules: +Install the following python modules (it is probably wise to use a local +Python with environment for this) * Flask * pyyaml @@ -53,12 +60,14 @@ SECRET_HMAC_CODE = '*' ``` ```sh +# Use a working copy of python +export python=$HOME/ve27/bin/python export WQFLASK_SETTINGS=$HOME/settings.py source /home/pjotr/ve27/bin/activate cd genenetwork2/wqflask -python ./runserver.py +$python ./runserver.py or -python ./secure_server.py +$python ./secure_server.py ``` diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index b2067b27..98bbead8 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -856,7 +856,7 @@ def gwas_with_redis(key,species,new_code=True): print(key) v = params[key] if v is not None: - v = np.array(v) + v = np.array(v).astype(np.float) return v def narrayT(key): @@ -969,6 +969,6 @@ if __name__ == '__main__': if has_gn2: gn2_main() else: - print("Run from runlmm.py instead") + fatal("Run from runlmm.py instead") |