WindowMasker: Difference between revisions
From genomewiki
Jump to navigationJump to search
(windowmasker installation notes) |
No edit summary |
||
| Line 18: | Line 18: | ||
cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker | cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker | ||
cp README /cluster/bin/man/man1/winmasker.1 | 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''. | |||
Revision as of 22:00, 6 April 2006
WindowMasker is a denovo repeat finder from the NCBI, published in 2006.
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.
