WindowMasker: Difference between revisions
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WindowMasker is a [[denovo repeat finder]] from the NCBI, published in 2006. | WindowMasker is a [[denovo repeat finder]] from the NCBI, published in 2006<ref>Morgulis A, Gertz EM, Schaffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=16287941&dopt=Abstract PubMed]</ref>. | ||
== UCSC Installation == | |||
It was taken from the NCBI C++ Toolkit (Dec. 2005) and installed into | |||
/cluster/bin/x86_64 | |||
the following way: | |||
ssh kolossus | |||
cd /scratch/andy | |||
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--Dec_31_2005.tar.gz | |||
tar xfz ncbi_cxx--Dec_31_2005.tar.gz | |||
cd ncbi_cxx--Dec_31_2005 | |||
./configure --without-debug --with-optimization --with-projects=src/app/winmasker/windowmasker.lst | |||
cd /scratch/andy/ncbi_cxx--Dec_31_2005/GCC344-Release64/build && make all_p | |||
cd app/winmasker/ | |||
cp windowmasker /cluster/bin/x86_64/ | |||
The README file in src/app/winmasker looks enough like a '''man''' file so | |||
cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker | |||
cp README /cluster/bin/man/man1/winmasker.1 | |||
== Opossum Experiment == | |||
*Running chr8 on hgwdev64 took about 5 min. Not bad. | |||
*Trying this thing genome-wide was a problem. It was never using more than 2 gigs of RAM and after about 2.5 hours it errored. | |||
*Running on the pitakluster was a problem too. Apparently this program communicates with the NCBI over the internet. ''Seems a little suspicious''. | |||
*The results of the one-chromosome-at-a-time run on kolossus: | |||
real 228m34.868s | |||
user 72m38.388s | |||
sys 15m1.872s | |||
== References == | |||
<references/> | |||
[[Category:Technical FAQ]] | |||
Latest revision as of 23:21, 14 August 2006
WindowMasker is a denovo repeat finder from the NCBI, published in 2006[1].
UCSC Installation
It was taken from the NCBI C++ Toolkit (Dec. 2005) and installed into
/cluster/bin/x86_64
the following way:
ssh kolossus cd /scratch/andy wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--Dec_31_2005.tar.gz tar xfz ncbi_cxx--Dec_31_2005.tar.gz cd ncbi_cxx--Dec_31_2005 ./configure --without-debug --with-optimization --with-projects=src/app/winmasker/windowmasker.lst cd /scratch/andy/ncbi_cxx--Dec_31_2005/GCC344-Release64/build && make all_p cd app/winmasker/ cp windowmasker /cluster/bin/x86_64/
The README file in src/app/winmasker looks enough like a man file so
cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker cp README /cluster/bin/man/man1/winmasker.1
Opossum Experiment
- Running chr8 on hgwdev64 took about 5 min. Not bad.
- Trying this thing genome-wide was a problem. It was never using more than 2 gigs of RAM and after about 2.5 hours it errored.
- Running on the pitakluster was a problem too. Apparently this program communicates with the NCBI over the internet. Seems a little suspicious.
- The results of the one-chromosome-at-a-time run on kolossus:
real 228m34.868s user 72m38.388s sys 15m1.872s
