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| for_members [2019/12/17 16:44] – [General guidelines for conducting research in the Oncinfo Lab] admin | for_members [2020/02/03 22:47] – [General guidelines for conducting research in the Oncinfo Lab] admin |
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| - 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. | - 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. We usually use Lonestar5 for computing and Ranch for storage of large data. A simple test for running a job on the Lonestar 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>@ls5.tacc.utexas.edu \\ $ cd ~zare \\ login1.ls5(1099)$ cat ./test.sh'' \\ ''login1.ls5(1099)$ sbatch ./test.sh'' \\ You can monitor your jobs using ''squeue -u <usrname>''. \\ The above command will submit the job to the development queue. If you want to submit a job to the normal queue, you can do the following: \\ ''login1.ls5(1099)$ sbatch -p normal -n 1 -t 2 ./test.sh'' |
| - Every member should upload their photo to his profile in the wiki. Todo this, click on your username at the top right, then, Account. In addition, everyone should have a photo and their updated CV in pdf format on their personal page. [[:file_view_cv_template.zip_543305154_cv_template.zip|This]] is an optional LaTeX template. The permission of any lab notebook (lano) should be set to "hidden"and it is important that they be updated EVERY day. [[https://civihosting.com/|CiviHosting]] provides us with two edit modes: ckg and DW. Use the one that is more convenient for you. Write your posts in anti-chronological order so that the newest post comes at the top. For facilitating future reference, avoid sending data as attachments. Instead, upload files to your lano and link to them where needed. | - Every member should upload their photo to his profile in the wiki. Todo this, click on your username at the top right, then, Account. In addition, everyone should have a photo and their updated CV in pdf format on their personal page. [[:file_view_cv_template.zip_543305154_cv_template.zip|This]] is an optional LaTeX template. The permission of any lab notebook (lano) should be set to "hidden"and it is important that they be updated EVERY day. [[https://civihosting.com/|CiviHosting]] provides us with two edit modes: ckg and DW. Use the one that is more convenient for you. Write your posts in anti-chronological order so that the newest post comes at the top. For facilitating future reference, avoid sending data as attachments. Instead, upload files to your lano and link to them where needed. |
| - You can install Google Scholar [[https://chrome.google.com/webstore/detail/google-scholar-button/ldipcbpaocekfooobnbcddclnhejkcpn?hl=en|Button]] add-on for an easier way of searching Google Scholar. You select the paper title and then click on the little blue icon on the top right corner. For any paper which you want to cite on the lab wiki, find it on Google Scholar, click on "More>Cite" and copy the MLA format. Also, use [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]] for easy citation in Google doc, and Math [[https://gsuite.google.com/marketplace/app/math_equations/825973477142|Equations]] for writing and manipulating equations on Google presentations. | - You can install Google Scholar [[https://chrome.google.com/webstore/detail/google-scholar-button/ldipcbpaocekfooobnbcddclnhejkcpn?hl=en|Button]] add-on for an easier way of searching Google Scholar. You select the paper title and then click on the little blue icon on the top right corner. For any paper which you want to cite on the lab wiki, find it on Google Scholar, click on "More>Cite" and copy the MLA format. Also, use [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]] for easy citation in Google doc, and Math [[https://gsuite.google.com/marketplace/app/math_equations/825973477142|Equations]] for writing and manipulating equations on Google presentations. |
