Panflam

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-	OS : Ubuntu Server 9.04	+	==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.
-	Installed Softwares	+	==Hardware==
-	*build-essential gcj gfortran automake ia32-libs g++-multilib libc6-dev-i386 alien rpm libstdc++5	+	*add RAM : 4GB X 4
-	*sbackup	+	**Total RAM: 32GB (4GB X 8)
-	*NFS	+	*add 1TB disk : /home4
-	2009.09.27	+
-	*X11vnc server&viewer	+	/home 1TB : tools, working
-	2009.09.28	+
-	*glimmer&ELPH	+	/home2 500GB : data
-	*virtualbox (to install manatee)	+
-	*Manatee (at virtualbox)	+	/home3 1TB : [[panflam_backup |backup]]
-	2009.09.29	+
-	*tRNAscan-SE	+	/home4 : additional working folder
-	2009.09.30	+
-	*Biopython	+	==OS==
-	*BER	+	*Ubuntu Server 9.04
-	*cdbtools	+	*Intel Xeon Dual-Quadcore (8 cores)
-	*blast2 (apt-get으로 설치) [NCBI]	+
-	*Bioperl	+	==Installed Softwares==
-	2009.10.7	+	*2012.12.10
-	*diya	+	**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
		+	**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		**Perl Module - XML::Simple Data::Merger
	**Infernal: inference of RNA alignments		**Infernal: inference of RNA alignments
	**pfamscan.pl		**pfamscan.pl
-	2009.10.?	+	*2009.09.30
-	*HMMER	+	**Biopython
-	2009.10.16	+	**BER
-	*RNAMMER	+	**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

---

Latest revision as of 08:14, 10 December 2012

Contents 1 Log 2 Hardware 3 OS 4 Installed Softwares

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
  • 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
  • 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)
  • 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