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server { | |
listen 80; | |
server_name localhost; | |
location / { | |
proxy_pass http://localhost:3000; | |
proxy_set_header X-Real-IP $remote_addr; | |
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; | |
proxy_set_header Host $host; | |
proxy_read_timeout 100m; |
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1. Login to VM as user who will be changed | |
1. use command 'id' to list current user's ids. Writedown current(old) UID and GID | |
2. determine what your new username's ids will be. If you already have an account in the sgn network, ssh into solanine and run 'cat /etc/passwd' to see what you systemwide ids are | |
3. change password with command 'passwd' | |
4. 'sudo su' to become superuser | |
4.5 for the following commands, it may be necessary to first stop all processes associated with the user to be changed, by running 'killall --user <OLDUSERNAME>' | |
5. 'usermod -l <NEWUSERNAME> -m -d <PATH/TO/NEW/HOMEDIR> <OLDUSERNAME>' to rename username and homedir | |
6. 'groupmod -n <NEWUSERNAME> <OLDUSERNAME>' to rename group | |
7. 'usermod -u <NEWUID> <USERNAME>' to change UID |
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server { | |
listen 80; | |
server_name localhost; | |
return 301 https://$host$request_uri; | |
} | |
server { | |
listen 443 default_server; |
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## Ref seq | |
cd to /export/prod/jbrowse_cassavabase/JBrowse-1.11.6/data/json | |
sudo mkdir cassavaV6_1 | |
cd into it | |
Downloaded Mesculenta_305_v6.fa.gz from JGI <http://genome.jgi.doe.gov/pages/dynamicOrganismDownlo\ | |
ad.jsf?organism=Mesculenta> | |
sudo bin/prepare-refseqs.pl --fasta Mesculenta_305_v6.fa.gz | |
sudo mv data/* . | |
sudo rm -r data |
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ssh production@172.30.2.197 | |
cd /export/prod/jbrowse_cassavabase/current/data | |
sudo mkdir cassava_example | |
cd cassava_example/ | |
sudo mkdir data_files | |
cd data_files/ | |
sudo ln -s /export/prod/public_cassava/Manihot_v6.1/ . | |
cd ../ | |
sudo ../../bin/prepare-refseqs.pl --fasta data_files/Manihot_v6.1/assembly/Mesculenta_305_v6.fa | |
sudo mv data/* . |
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to dump production db: | |
from commandline: pg_dump -U postgres -h db5.sgn.cornell.edu cxgn_musabase | db5.cxgn_musabase.pgsql.gz | |
to rename old test db: | |
ALTER DATABASE sandbox_musabase RENAME TO sandbox_musabase_backup | |
if there is an error, check for active processes: SELECT * FROM pg_stat_activity; | |
and force disconnect of processes (should be idle!): | |
SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE pid <> pg_backend_pid( ) AND datname = 'sandbox_musabase'; | |
the run ALTER command again, or remove it: | |
DROP DATABASE sandbox_musabase; |
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query for no misisng values: | |
SELECT table1.accession_id, table1.accession_name, table1.trait1, table2.trait2, table3.trait3 from (SELECT accession_id, accession_name, avg(phenotype_value::real) as trait1 FROM materialized_phenoview WHERE trial_id = 122 AND trait_id = 70741 group by 1,2) as table1 join (SELECT accession_id, accession_name, avg(phenotype_value::real) as trait2 FROM materialized_phenoview WHERE trial_id = 122 AND trait_id = 70691 group by 1,2) as table2 using(accession_id) join (SELECT accession_id, accession_name, avg(phenotype_value::real) as trait3 FROM materialized_phenoview WHERE trial_id = 122 AND trait_id = 70762 group by 1,2) as table3 using(accession_id) order by 2; | |
query for allowing missing values: | |
SELECT table0.accession_id, table0.accession_name, table1.trait1, table2.trait2, table3.trait3 from (SELECT accession_id, accession_name from materialized_phenoview WHERE trial_id = 122 group by 1,2) as table0 full outer join (SELECT accession_id, accession_name, avg(phenotype_value::re |
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ssh production@vm-04.sgn.cornell.edu | |
sudo xl list | |
sudo xl destroy hidap.sgn.cornell.edu | |
sudo xl create /etc/xen/hidap.sgn.cornell.edu.cfg | |
ssh production@hidap.sgn.cornell.edu | |
sudo systemctl restart shiny-server |
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sudo R | |
update.packages(ask=TRUE) | |
install.packages('devtools') | |
devtools::install_github('c5sire/brapi') | |
quit() |
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commit and push, or pull all branches to be included in update into master branch. | |
1. run tests, including unit, unit fixture, and selenium tests. | |
- for unit tests: `perl t/test_fixture.pl --noserver t/unit` | |
- for unit_fixture tests: `perl t/test_fixture.pl t/unit_fixture | |
- for selenium tests: | |
run selenium2 server in seperate terminal with `java -jar selenium-server-standalone-2.53.0.jar`. This jar file should be in the vagrant home directory | |
then run `perl t/test_fixture.pl t/selenium2/` | |
if any tests fail, they can be run individually and troubleshot to make any necessary fixes to the code on the master branch, or to update the test itself |
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