Installation

1. git clone

git clone git@github.com:CCRGeneticsBranch/Oncogenomics_v2.git clinomics

1. composer install

cd clinomics mkdir -p bootstrap/cache composer update composer install

1. change storage permission mkdir -p storage/logs mkdir -p storage/framework/views mkdir -p storage/framework/cache chmod g+w storage/logs chmod g+w storage/framework/views chmod g+w storage/framework/cache
2. set sitedata link ``` ln -s /mnt/projects/CCR-JK-oncogenomics/static/sitedata/dev/ sitedata cd app ln -s ../sitedata/app/bin . ln -s ../sitedata/app/metadata . ln -s ../sitedata/app/ref . ln -s ../sitedata/app/scripts . cd ../storage ln -s ../sitedata/storage/bams . ln -s ../sitedata/storage/dataintegrityreport . ln -s ../sitedata/storage/ProcessedResults . ln -s ../sitedata/storage/projectdata . ln -s ../sitedata/storage/sync . cd ../public ln -s ../sitedata/app/ref . cd .. ```
3. edit .env file

``` APPNAME=Laravel APPENV=local APPKEY= APPDEBUG=true APP_URL=https://fsabcl-onc01d.ncifcrf.gov

LOGCHANNEL=stack LOGDEPRECATIONSCHANNEL=null LOGLEVEL=debug

DBCONNECTION=oracle DBHOST= DBPORT= DBDATABASE= DBUSERNAME= DBPASSWORD=

ISPUBLICSITE=0 AUTHREDIRECT=https://fsabcl-onc01d.ncifcrf.gov/clinomicsd/public/login AUTHOATH=https://stsstg.nih.gov/auth/oauth/v2/authorize AUTHCLIENTID= AUTHCLIENTSECRETE= AUTHSCOPE=email+profile+openid AUTHWEBSITE=https://stsstg.nih.gov URL=https://fsabcl-onc01t.ncifcrf.gov/clinomicsd/public URLPRODUCTION=https://oncogenomics.ccr.cancer.gov/production/public URLPUBLIC=https://clinomics.ccr.cancer.gov/clinomics/public/ URLDEV=https://fsabcl-onc01d.ncifcrf.gov/clinomicsdev/public RLIBS=/mnt/nasapps/development/R/rlibs/4.0.2/ RPATH=/mnt/nasapps/development/R/4.0.2/bin/ LDLIBRARYPATH=/mnt/nasapps/development/R/sharedlibs/4.0.2 MOUNT=/mnt/projects/CCR-JK-oncogenomics/static/clones/clinomics MOUNTPUBLIC=/mnt/projects/CCR-JK-oncogenomics/static/clones/clinomicspublic AVIA=true TOKEN= PUBLIC_TOKEN=

BROADCASTDRIVER=log CACHEDRIVER=file FILESYSTEMDRIVER=local QUEUECONNECTION=sync SESSIONDRIVER=cookie SESSIONLIFETIME=86400 SESSIONSECURECOOKIE=true

MEMCACHED_HOST=127.0.0.1

REDISHOST=127.0.0.1 REDISPASSWORD=null REDIS_PORT=6379

MAILFROMADDRESS=oncogenomics@mail.nih.gov MAILMAILER=sendmail MAILHOST=mailfwd.nih.gov MAILPORT=587 MAILUSERNAME=null MAILPASSWORD=null MAILENCRYPTION=tls MAILFROMNAME=Oncogenomics

AWSACCESSKEYID= AWSSECRETACCESSKEY= AWSDEFAULTREGION=us-east-1 AWSBUCKET= AWSUSEPATHSTYLE_ENDPOINT=false

PUSHERAPPID= PUSHERAPPKEY= PUSHERAPPSECRET= PUSHERAPPCLUSTER=mt1

MIXPUSHERAPPKEY="${PUSHERAPPKEY}" MIXPUSHERAPPCLUSTER="${PUSHERAPPCLUSTER}" ```