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for_members [2019/01/09 16:21] – [General guidelines for conducting research in Oncinfo lab] adminfor_members [2019/01/09 18:48] – [General guidelines for conducting research in Oncinfo lab] admin
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   - Any file or data on this wiki that has restricted permissions, such as some paper pdfs or drafts, should not be shared with nonmembers unless authorized by the PI.   - Any file or data on this wiki that has restricted permissions, such as some paper pdfs or drafts, should not be shared with nonmembers unless authorized by the PI.
   - All members should read and follow [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424|Bill's]] guidelines, and organize their files and folders accordingly and to some extend. Start by making a "~/proj" directory in your home folder that will eventually contain a subfolder for each project you are working on. Major subfolders must have a readme file for example to describe where the data is coming from. Your code folder must include a runall.R script that sources other scripts. Avoid sourcing scripts in other scripts except for the runall because then following and debugging the pipeline would be difficult.   - All members should read and follow [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424|Bill's]] guidelines, and organize their files and folders accordingly and to some extend. Start by making a "~/proj" directory in your home folder that will eventually contain a subfolder for each project you are working on. Major subfolders must have a readme file for example to describe where the data is coming from. Your code folder must include a runall.R script that sources other scripts. Avoid sourcing scripts in other scripts except for the runall because then following and debugging the pipeline would be difficult.
-  - Your code and documents should be stored in a Bitbucket repository like [[https://bitbucket.org/habilzare/genetwork|https://bitbucket.org/habilzare/genetwork]]. Sign up for an [[https://bitbucket.org/account/signup/|account]] and sent your username to Habil. Do not forget to add your photo. If you are new to Bitbucket, take [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]]. You can [[https://confluence.atlassian.com/bitbucket/use-the-ssh-protocol-with-bitbucket-cloud-221449711.html|avoid]] having to manually type a password each time you pull using ssh. To add a key, click on your photo at the top right corner of Bitbucket page, Bitbucket settings, SSH keys, Add key. This trick is not appropriate for TACC clusters because we should not change our .ssh folder there. On the cluster, use https to clone instead of ssh. Do NOT skip this step. Before changing anything in a repository, read and abide to the conventions described in the main readme file.+  - Your code and documents should be stored in a Bitbucket repository like [[https://bitbucket.org/habilzare/genetwork|https://bitbucket.org/habilzare/genetwork]]. Sign up for an [[https://bitbucket.org/account/signup/|account]] and add your photo. Only then, send your username to Habil. If you are new to Bitbucket, take [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]]. You can [[https://confluence.atlassian.com/bitbucket/use-the-ssh-protocol-with-bitbucket-cloud-221449711.html|avoid]] having to manually type a password each time you pull using ssh. To add a key, click on your photo at the top right corner of Bitbucket page, Bitbucket settings, SSH keys, Add key. This trick is not appropriate for TACC clusters because we should not change our .ssh folder there. On the cluster, use https to clone instead of ssh. Do NOT skip this step. Before changing anything in a repository, read and abide to the conventions described in the main readme file.
   - Do NOT use space in the file or folder names. Do NOT include binary files such as png, pdf, RData, etc. in a Bitbucket repository unless on an exceptional basis. Instead, use e.g., ''rsync -avz -e ssh <usrname>@ls5.tacc.utexas.edu''  or ''scp ''to transfer files, and document the exact paths in a readme file in the corresponding folder.   - Do NOT use space in the file or folder names. Do NOT include binary files such as png, pdf, RData, etc. in a Bitbucket repository unless on an exceptional basis. Instead, use e.g., ''rsync -avz -e ssh <usrname>@ls5.tacc.utexas.edu''  or ''scp ''to transfer files, and document the exact paths in a readme file in the corresponding folder.
   - If you want to use TACC resources, you first [[https://portal.tacc.utexas.edu/account-request|create]] an account, and then ask Habil to add you to a project. A simple test for running a job on Stampede cluster is the following. Look at their user [[https://portal.tacc.utexas.edu/user-guides/stampede|guide]] or [[https://srcc.stanford.edu/sge-slurm-conversion|this]] table of commands for more details. \\  $ ssh <username>@stampede.tacc.utexas.edu \\  $ cd ~zare \\  login4.stampede(1)$ sbatch -p normal -n 1 -t 3 ./test.sh \\  We usually use Lonestar5 for computing and Ranch for storage of large data.   - If you want to use TACC resources, you first [[https://portal.tacc.utexas.edu/account-request|create]] an account, and then ask Habil to add you to a project. A simple test for running a job on Stampede cluster is the following. Look at their user [[https://portal.tacc.utexas.edu/user-guides/stampede|guide]] or [[https://srcc.stanford.edu/sge-slurm-conversion|this]] table of commands for more details. \\  $ ssh <username>@stampede.tacc.utexas.edu \\  $ cd ~zare \\  login4.stampede(1)$ sbatch -p normal -n 1 -t 3 ./test.sh \\  We usually use Lonestar5 for computing and Ranch for storage of large data.