aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/webqtlConfig.py
diff options
context:
space:
mode:
authorZachary Sloan2013-08-14 17:25:52 -0500
committerZachary Sloan2013-08-14 17:25:52 -0500
commit26b1883a8fe4053b59833178f44e047157f2fc9c (patch)
treed2359e5952f6062d75ba1f43f1804a7b6df284c9 /wqflask/base/webqtlConfig.py
parenteea1c38a9851f31011787b27c14365211a06ea51 (diff)
parent6379959af53b2ec595b85ccdc099c6f14adf0381 (diff)
downloadgenenetwork2-26b1883a8fe4053b59833178f44e047157f2fc9c.tar.gz
Merge branch 'master' of https://github.com/zsloan/genenetwork
Diffstat (limited to 'wqflask/base/webqtlConfig.py')
-rwxr-xr-xwqflask/base/webqtlConfig.py11
1 files changed, 6 insertions, 5 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index a811c3cd..23d32233 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -1,4 +1,3 @@
-from webqtlConfigLocal import *
#########################################'
# Environment Variables - public
#########################################
@@ -36,7 +35,7 @@ NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrie
UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"
+UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
@@ -49,15 +48,17 @@ UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s
GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
+
+GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later
SECUREDIR = GNROOT + 'secure/'
COMMON_LIB = GNROOT + 'support/admin'
HTMLPATH = GNROOT + 'web/'
-PYLMM_PATH = '/home/zas1024/'
-SNP_PATH = '/mnt/xvdf1/snps/'
+PYLMM_PATH = '/home/zas1024/plink/'
+SNP_PATH = '/home/zas1024/snps/'
IMGDIR = HTMLPATH +'image/'
IMAGESPATH = HTMLPATH + 'images/'
UPLOADPATH = IMAGESPATH + 'upload/'
-TMPDIR = HTMLPATH + 'tmp/'
+TMPDIR = '/tmp/'
GENODIR = HTMLPATH + 'genotypes/'
NEWGENODIR = HTMLPATH + 'new_genotypes/'
GENO_ARCHIVE_DIR = GENODIR + 'archive/'