diff options
| -rw-r--r-- | misc/gn_installation_notes.txt | 40 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfigLocal.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 176 |
4 files changed, 131 insertions, 91 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index 7545a5b8..913021db 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -181,6 +181,46 @@ ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key ============================================ +Installing redis server + +In the dls directory: +$ wget http://redis.googlecode.com/files/redis-2.6.14.tar.gz +$ tar xzf redis-2.6.14.tar.gz +$ cd redis-2.6.14 +$ make + +Run redis (from inside redis-2.6.14 directory): +src/redis-server + +For the rest of the installation instructions, refer to: +http://redis.io/topics/quickstart + +To continue installation (from the README): + +In order to install Redis binaries into /usr/local/bin just use: + + % make install + +Make install will just install binaries in your system, but will not configure +init scripts and configuration files in the appropriate place. This is not +needed if you want just to play a bit with Redis, but if you are installing +it the proper way for a production system, we have a script doing this +for Ubuntu and Debian systems: + + % cd utils + % ./install_server + +The script will ask you a few questions and will setup everything you need +to run Redis properly as a background daemon that will start again on +system reboots. + +In the redis config file (/etc/redis/6379.conf) uncomment the following line: +bind 127.0.0.1 + +This is so only the local computer has access + +============================================ + Using Yolk Install Yolk: diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py index abaeff93..cc53866b 100755 --- a/wqflask/base/webqtlConfigLocal.py +++ b/wqflask/base/webqtlConfigLocal.py @@ -5,12 +5,12 @@ MYSQL_SERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' DB_NAME = 'db_webqtl' DB_USER = 'webqtl' -DB_PASSWD = 'f2ZypIflRM' +DB_PASSWD = 'zK150dVzyvclGY5aCzavcK' MYSQL_UPDSERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' DB_UPDNAME = 'db_webqtl' DB_UPDUSER = 'webqtl' -DB_UPDPASSWD = 'f2ZypIflRM' +DB_UPDPASSWD = 'zK150dVzyvclGY5aCzavcK' GNROOT = '/home/zas1024/gene/' ROOT_URL = 'http://50.16.251.170' diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 4c544192..b6bf5bfd 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -41,7 +41,6 @@ from pprint import pformat as pf from base import webqtlConfig - # build MySql database connection Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, @@ -148,6 +147,7 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + species = get_species() groups = get_groups(species) types = get_types(groups) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 88bdcb11..a4d88ab2 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -64,14 +64,14 @@ ], "Leaf": [ [ - "B1LI0809M5", - "Barley1 Leaf INOC TTKS (Aug09) MAS5" - ], - [ "B1LI0809R", "Barley1 Leaf INOC TTKS (Aug09) RMA" ], [ + "B1LI0809M5", + "Barley1 Leaf INOC TTKS (Aug09) MAS5" + ], + [ "B1MI0809M5", "Barley1 Leaf MOCK TTKS (Aug09) MAS5" ], @@ -114,12 +114,12 @@ "Barley1 Leaf MAS 5.0 SCRI (Dec06)" ], [ - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ], - [ "B30_K_1206_Rn", "Barley1 Leaf gcRMAn SCRI (Dec06)" + ], + [ + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" ] ], "Phenotypes": [ @@ -212,14 +212,14 @@ "AD-cases-controls-Myers": { "Brain": [ [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ "GSE15222_F_A_RI_0409", "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" ], [ + "GSE15222_F_N_RI_0409", + "GSE15222 Human Brain Normal Myers (Apr09) RankInv" + ], + [ "GSE15222_F_RI_0409", "GSE15222 Human Brain Myers (Apr09) RankInv" ] @@ -548,12 +548,12 @@ "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], [ - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ], - [ "MA_M_0704_R", "NCI Mammary mRNA M430 (July04) RMA" + ], + [ + "MA_M_0704_M", + "NCI Mammary mRNA M430 (July04) MAS5" ] ], "Phenotypes": [ @@ -598,12 +598,12 @@ ], "Liver": [ [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ "LVF2_M_0704_R", "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + ], + [ + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" ] ], "Phenotypes": [ @@ -632,12 +632,12 @@ "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ "BRF2_M_0304_R", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + ], + [ + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" ] ], "Genotypes": [ @@ -728,44 +728,44 @@ ], "Striatum": [ [ + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" + ], + [ "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" ], [ "SA_M2_0905_P", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "BHF2": { "Adipose": [ [ - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ "UCLA_BHF2_ADIPOSE_MALE", "UCLA BHF2 Adipose Male mlratio" ], [ + "UCLA_BHF2_ADIPOSE_FEMALE", + "UCLA BHF2 Adipose Female mlratio" + ], + [ "UCLA_BHF2_ADIPOSE_0605", "UCLA BHF2 Adipose (June05) mlratio" ] ], "Brain": [ [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ "UCLA_BHF2_BRAIN_MALE", "UCLA BHF2 Brain Male mlratio" ], [ + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], + [ "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" ] @@ -778,28 +778,28 @@ ], "Liver": [ [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ "UCLA_BHF2_LIVER_MALE", "UCLA BHF2 Liver Male mlratio" ], [ + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ "UCLA_BHF2_LIVER_0605", "UCLA BHF2 Liver (June05) mlratio" ] ], "Muscle": [ [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ "UCLA_BHF2_MUSCLE_MALE", "UCLA BHF2 Muscle Male mlratio **" ], [ + "UCLA_BHF2_MUSCLE_FEMALE", + "UCLA BHF2 Muscle Female mlratio **" + ], + [ "UCLA_BHF2_MUSCLE_0605", "UCLA BHF2 Muscle (June05) mlratio **" ] @@ -924,6 +924,10 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + ], + [ "BR_U_0805_R", "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], @@ -932,10 +936,6 @@ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" ] @@ -956,6 +956,10 @@ ], "Cerebellum": [ [ + "CB_M_1004_M", + "SJUT Cerebellum mRNA M430 (Oct04) MAS5" + ], + [ "CB_M_1004_R", "SJUT Cerebellum mRNA M430 (Oct04) RMA" ], @@ -964,10 +968,6 @@ "SJUT Cerebellum mRNA M430 (Oct04) PDNN" ], [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], - [ "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" ] @@ -1132,12 +1132,12 @@ "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" ], [ - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], - [ "MA_M2_0706_P", "Mouse Kidney M430v2 (Jul06) PDNN" + ], + [ + "MA_M2_0706_R", + "Mouse Kidney M430v2 (Jul06) RMA" ] ], "Leucocytes": [ @@ -1156,6 +1156,10 @@ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" ], [ + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" + ], + [ "GenEx_BXD_liverEt_M5F_0912", "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" ], @@ -1164,10 +1168,6 @@ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males **" ], [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ "GenEx_BXD_liverSal_RMA_M_0211", "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" ], @@ -1228,14 +1228,14 @@ ], "Neocortex": [ [ - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" - ], - [ "DevNeocortex_ILM6.2P14RInv_1111", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" ], [ + "DevNeocortex_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" + ], + [ "HQFNeoc_1210v2_RankInv", "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" ], @@ -1248,12 +1248,12 @@ "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], [ - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" - ], - [ "DevNeocortex_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" + ], + [ + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens": [ @@ -1294,6 +1294,10 @@ ], "Prefrontal Cortex": [ [ + "VCUEtOH_1206_R", + "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + ], + [ "VCUSal_1206_R", "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" ], @@ -1302,10 +1306,6 @@ "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" ], [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], - [ "VCU_PF_Air_0111_R", "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" ], @@ -1448,16 +1448,16 @@ ], "Ventral Tegmental Area": [ [ + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" + ], + [ "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" ], [ "VCUEtvsSal_0609_R", "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **" - ], - [ - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" ] ] }, @@ -1574,12 +1574,12 @@ ], "Hippocampus": [ [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ "HC_M2CB_1205_R", "Hippocampus Consortium M430v2 CXB (Dec05) RMA" + ], + [ + "HC_M2CB_1205_P", + "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], "Phenotypes": [ @@ -1712,16 +1712,16 @@ ], "Prefrontal Cortex": [ [ + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" + ], + [ "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" ], [ "VCUEt_vs_Sal_0806_R", "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" - ], - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" ] ] }, @@ -1734,12 +1734,12 @@ ], "Hippocampus": [ [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" ] ], "Liver": [ |