Panflam
From CSBLwiki
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
