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for_members [2019/12/13 17:06] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2019/12/13 17:06] – [General guidelines for conducting research in the Oncinfo Lab] admin
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   - For future reference, please add the link to your presentations and drafts on the [[https://oncinfo.org/drafts|drafts]] page. At a minimum, please include: the author, the date, the audience, and the subject.   - For future reference, please add the link to your presentations and drafts on the [[https://oncinfo.org/drafts|drafts]] page. At a minimum, please include: the author, the date, the audience, and the subject.
   - 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 add your photo. Do NOT sign in using your Google account. Only then, send your username to Habil. If you are new to Bitbucket, spend an hour on the [[https://confluence.atlassian.com/bitbucket/tutorial-learn-bitbucket-with-git-759857287.html|tutorial]]. Taking [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]] is NOT needed for beginers. 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 mess up with other's git folders on the cluster. You should //only//  clone, pull, and push in your own home or work directory. 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. Do NOT sign in using your Google account. Only then, send your username to Habil. If you are new to Bitbucket, spend an hour on the [[https://confluence.atlassian.com/bitbucket/tutorial-learn-bitbucket-with-git-759857287.html|tutorial]]. Taking [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]] is NOT needed for beginners. 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 mess up with other's git folders on the cluster. You should //only//  clone, pull, and push in your own home or work directory. 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.