From 97ccc478543a7bb08fe0cf178e320dd5811d8bfa Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Feb 2018 07:53:53 +0000
Subject: Check for bimbam path and bail out if it is missing

---
 bin/genenetwork2 | 1 +
 1 file changed, 1 insertion(+)

(limited to 'bin')

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)
 
-- 
cgit v1.2.3


From 91365baf9ba657f56c19201874cdf60aede75dd1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Feb 2018 08:53:27 +0000
Subject: Fixing GEMMA LOCO

---
 bin/genenetwork2                                   |  4 +++-
 wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++++++---
 2 files changed, 11 insertions(+), 4 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 7148c022..52144f4d 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -121,7 +121,9 @@ 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"
+    if [ -z GEMMA_WRAPPER_COMMAND ]; then
+        export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    fi
     if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
     if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
     if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index c004983e..68920130 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,7 +3,7 @@ import os, math, string, random, json
 from base import webqtlConfig
 from base.trait import GeneralTrait
 from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
 
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
@@ -210,8 +210,13 @@ def parse_gemma_output(genofile_name):
 def parse_loco_output(this_dataset, gwa_output_filename):
 
     output_filelist = []
-    with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
-       data = json.load(data_file)
+    jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json"
+    assert_file(jsonfn)
+    try:
+        with open(jsonfn) as data_file:
+            data = json.load(data_file)
+    except:
+        logger.error("Can not parse "+jsonfn)
 
     files = data['files']
     for file in files:
-- 
cgit v1.2.3


From 7009d382c4515340cc7080192c58cc3fc0c1ced2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Feb 2018 09:38:22 +0000
Subject: Fix env variable $GEMMA_WRAPPER_COMMAND

---
 bin/genenetwork2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 52144f4d..d1b8d25f 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -121,7 +121,7 @@ else
     export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
     export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
-    if [ -z GEMMA_WRAPPER_COMMAND ]; then
+    if [ -z $GEMMA_WRAPPER_COMMAND ]; then
         export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
     fi
     if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
-- 
cgit v1.2.3


From 7f3a493db99998992f86af9a5e333103f255be6d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sun, 11 Feb 2018 11:26:01 +0100
Subject: Using eventlet workers

---
 bin/genenetwork2 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d1b8d25f..2f0b841e 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -192,7 +192,8 @@ if [ "$1" = '-gunicorn-prod' ] ; then
     cd $GN2_BASE_DIR/wqflask
     echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
-    cmd="--bind 0.0.0.0:$SERVER_PORT --workers=32 --max-requests 1000 --timeout 1200 wsgi"
+    cmd="--bind 0.0.0.0:$SERVER_PORT -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
+    # cmd="--bind 0.0.0.0:$SERVER_PORT --workers 20 --keep-alive 75 --max-requests 1000 --timeout 1200 wsgi"
     echo RUNNING gunicorn $cmd
     gunicorn $cmd
     exit $?
-- 
cgit v1.2.3


From 018c9d6c50e90d783bc7bd1b2a0d85b080ebf394 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 11 Feb 2018 11:37:36 +0000
Subject: Added gunicorn pid so we can not run twice

---
 bin/genenetwork2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 2f0b841e..8886e4bc 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -192,8 +192,8 @@ if [ "$1" = '-gunicorn-prod' ] ; then
     cd $GN2_BASE_DIR/wqflask
     echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
-    cmd="--bind 0.0.0.0:$SERVER_PORT -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
-    # cmd="--bind 0.0.0.0:$SERVER_PORT --workers 20 --keep-alive 75 --max-requests 1000 --timeout 1200 wsgi"
+    PID=$TMPDIR/gunicorn.$USER.pid
+    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
     echo RUNNING gunicorn $cmd
     gunicorn $cmd
     exit $?
-- 
cgit v1.2.3