Difference between revisions of "MSblender TACC"
From Marcotte Lab
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* Generally, 'longhorn' has shorter queue than 'lonestar'. So if you don't need large memory(> 4GB), use 'longhorn'. | * Generally, 'longhorn' has shorter queue than 'lonestar'. So if you don't need large memory(> 4GB), use 'longhorn'. | ||
* Always work at $SCRATCH directory, not at /corral or your $HOME. | * Always work at $SCRATCH directory, not at /corral or your $HOME. | ||
| + | * All source codes are available at /corral/utexas/A-cm10/src.MS/. | ||
| + | * All packages are installed at /corral/utexas/A-cm10/src.MS/local/. | ||
| + | * To run InsPecT, you need to set LD_LIBRARY_PATH for expat library. Type below command before running InsPecT (or put it on '$HOME/.profile_user' | ||
| + | <pre> $ export LD_LIBRARY_PATH="/corral/utexas/A-cm10/src.MS/local/lib/" </pre> | ||
| + | * Default python interpreter is 2.4 at TACC. You need to load 2.7.1 as below. | ||
| + | <pre> $ module load python</pre> | ||
== Currently installed packages == | == Currently installed packages == | ||
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* InsPecT (20120109) | * InsPecT (20120109) | ||
** /corral/utexas/A-cm10/src.MS/local/bin/inspect | ** /corral/utexas/A-cm10/src.MS/local/bin/inspect | ||
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== Install MS-toolbox & MSblender == | == Install MS-toolbox & MSblender == | ||
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$ git clone git@github.com:marcottelab/MSblender.git</pre> | $ git clone git@github.com:marcottelab/MSblender.git</pre> | ||
* You don't need to compile MSblender codes under 'src' directory. Executable file is already available at /corral/utexas/A-cm10/src.MS/local/bin/msblender. | * You don't need to compile MSblender codes under 'src' directory. Executable file is already available at /corral/utexas/A-cm10/src.MS/local/bin/msblender. | ||
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| + | == Let's start == | ||
| + | <pre>$ cd $SCRATCH | ||
| + | $ mkdir my-project | ||
| + | $ cd my-project | ||
| + | $ ~/git/MS-toolbox/bin/mstb-setup.py | ||
Revision as of 11:55, 14 February 2012
Contents |
Before you start
- To use this setting, your TACC account needs to be allocated to our lab project('A-cm10'). If you don't have an account, create it at https://portal.tacc.utexas.edu/. Then, ask Edward to assign your account as a member of lab project.
- Generally, 'longhorn' has shorter queue than 'lonestar'. So if you don't need large memory(> 4GB), use 'longhorn'.
- Always work at $SCRATCH directory, not at /corral or your $HOME.
- All source codes are available at /corral/utexas/A-cm10/src.MS/.
- All packages are installed at /corral/utexas/A-cm10/src.MS/local/.
- To run InsPecT, you need to set LD_LIBRARY_PATH for expat library. Type below command before running InsPecT (or put it on '$HOME/.profile_user'
$ export LD_LIBRARY_PATH="/corral/utexas/A-cm10/src.MS/local/lib/"
- Default python interpreter is 2.4 at TACC. You need to load 2.7.1 as below.
$ module load python
Currently installed packages
These packages are installed at lonestar.
- TPP-4.5.1 + X!Tandem (2010.10.01.1)
- /corral/utexas/A-cm10/src.MS/local/tppbin/xinteract (integrated wrapper for *Prophet)
- /corral/utexas/A-cm10/src.MS/local/tppbin/tandem (X!Tandem with k-score support)
- Crux 1.37
- /corral/utexas/A-cm10/src.MS/local/bin/crux
- Tide 1.0
- /corral/utexas/A-cm10/src.MS/local/bin/tide-index
- /corral/utexas/A-cm10/src.MS/local/bin/tide-msconvert
- /corral/utexas/A-cm10/src.MS/local/bin/tide-search
- MSGFDB (20120106)
- /corral/utexas/A-cm10/src.MS/MSGFDB/current/MSGFDB.jar
- InsPecT (20120109)
- /corral/utexas/A-cm10/src.MS/local/bin/inspect
Install MS-toolbox & MSblender
- I recommend to install MS-toolbox at your home individually, because everyone may want to use different search parameters.
$ module load git $ cd ~ $ mkdir git $ cd git $ git clone git@github.com:marcottelab/MS-toolbox.git $ git clone git@github.com:marcottelab/MSblender.git
- You don't need to compile MSblender codes under 'src' directory. Executable file is already available at /corral/utexas/A-cm10/src.MS/local/bin/msblender.
Let's start
$ cd $SCRATCH $ mkdir my-project $ cd my-project $ ~/git/MS-toolbox/bin/mstb-setup.py
