Panflam
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| + | ==Log== | ||
| + | *Create log_manager.py script (add to crontab (root) (0m, 0h, every day, every month)) | ||
| + | **Because the log files under the "/var/spool/PBS/" folder didn't removed automatically, it's space often jammed and no new log files can be created. | ||
| + | |||
| + | ==Hardware== | ||
| + | *add RAM : 4GB X 4 | ||
| + | **Total RAM: 32GB (4GB X 8) | ||
| + | *add 1TB disk : /home4 | ||
| + | |||
| + | /home 1TB : tools, working | ||
| + | |||
| + | /home2 500GB : data | ||
| + | |||
| + | /home3 1TB : [[panflam_backup |backup]] | ||
| + | |||
| + | /home4 : additional working folder | ||
| + | |||
==OS== | ==OS== | ||
*Ubuntu Server 9.04 | *Ubuntu Server 9.04 | ||
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==Installed Softwares== | ==Installed Softwares== | ||
| + | *2012.12.10 | ||
| + | **Galaxy : http://panpyro.korea.ac.kr:8080/ | ||
| + | ***참조 http://compbio.korea.ac.kr/roh329/?c=computer/16 | ||
| + | *2011.12.17 | ||
| + | **tRNAscan-SE -bug fix: perl -pi -e "s/getline/getline2/g" sqio.c | ||
| + | *2011.12.13 | ||
| + | **[http://pypi.python.org/pypi/ete2a1 ETE2] | ||
| + | *2011.08.17 | ||
| + | **pytable 2.2 | ||
| + | **numexpr 1.4.2 | ||
| + | **scipy 0.10 | ||
| + | **numpy 2.0.0 | ||
| + | **hdf5-1.8.7 | ||
| + | **Cython 1.5 | ||
| + | *2010.09.09 | ||
| + | **Berkeley DB library (for perl module DB_File) | ||
| + | **iprscan | ||
| + | **SignalP | ||
| + | **TMHMM | ||
| + | *2010.08.16 | ||
| + | **remove r-core, r-cran* | ||
| + | **libreadline-dev | ||
| + | **R-2.11.1 | ||
| + | *2010.07.27 | ||
| + | **BCBio (gff parser, gff writer) | ||
| + | *2010.07.17 | ||
| + | **SSAHA2 (for a PE mode of sff_extract) | ||
| + | **[http://bioinf.comav.upv.es/sff_extract/usage.html sff_extract] | ||
*2010.07.15 | *2010.07.15 | ||
**Primer3 (Dupfinisher,GapResolution dependency) | **Primer3 (Dupfinisher,GapResolution dependency) | ||
Latest revision as of 08:14, 10 December 2012
Contents |
Log
- Create log_manager.py script (add to crontab (root) (0m, 0h, every day, every month))
- Because the log files under the "/var/spool/PBS/" folder didn't removed automatically, it's space often jammed and no new log files can be created.
Hardware
- add RAM : 4GB X 4
- Total RAM: 32GB (4GB X 8)
- add 1TB disk : /home4
/home 1TB : tools, working
/home2 500GB : data
/home3 1TB : backup
/home4 : additional working folder
OS
- Ubuntu Server 9.04
- Intel Xeon Dual-Quadcore (8 cores)
Installed Softwares
- 2012.12.10
- 2011.12.17
- tRNAscan-SE -bug fix: perl -pi -e "s/getline/getline2/g" sqio.c
- 2011.12.13
- 2011.08.17
- pytable 2.2
- numexpr 1.4.2
- scipy 0.10
- numpy 2.0.0
- hdf5-1.8.7
- Cython 1.5
- 2010.09.09
- Berkeley DB library (for perl module DB_File)
- iprscan
- SignalP
- TMHMM
- 2010.08.16
- remove r-core, r-cran*
- libreadline-dev
- R-2.11.1
- 2010.07.27
- BCBio (gff parser, gff writer)
- 2010.07.17
- SSAHA2 (for a PE mode of sff_extract)
- sff_extract
- 2010.07.15
- Primer3 (Dupfinisher,GapResolution dependency)
- boulder (Dupfinisher dependency)
- Dupfinisher
- 2010.07.13
- biopython 1.54 upgrade
- 2010.07.06
- phred,phrap (/home/gnusnah/tools/UW/)
- 2010.07.05
- GapResolution
- 2010.06.15
- GapCloser(SOAP)
- Correction(SOAP)
- install: wgs-6.1 amd64
- install: MUMmer 3.22
- install: sparsehash
- install: abyss 1.2.0
- 2010.6.10
- velvet 0.7.63
- 2009.10.16
- RNAMMER
- 2009.10.?
- HMMER
- 2009.10.7
- diya
- Perl Module - XML::Simple Data::Merger
- Infernal: inference of RNA alignments
- pfamscan.pl
- 2009.09.30
- Biopython
- BER
- cdbtools
- blast2 (apt-get으로 설치) [NCBI]
- Bioperl
- 2009.09.29
- tRNAscan-SE
- 2009.09.28
- glimmer&ELPH
- virtualbox (to install manatee)
- Manatee (at virtualbox)
- 2009.09.27
- X11vnc server&viewer
- build-essential gcj gfortran automake ia32-libs g++-multilib libc6-dev-i386 alien rpm libstdc++5
- sbackup
- NFS
