Configuring STARS on Bio-Linux
Installing phrap
The distribution file should be named something like distrib.tar.Z.
Make a temporary directory 'phrap' and move the distribution file into it:
mkdir phrap
mv distrib.tar.Z phrap
cd phrap
You now need to uncompress the file:
uncompress distrib.tar.Z
tar xvf distrib.tar
To compile the program type:
make
To use phrap within STARS/Staden we need a modified version of phrap called 'gcphrap'. To compile this we need to download some files from the Staden website.
wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/phrap/phrap_extras.tar.gz
Uncompress these files and move them to the current phrap source directory
gzip -cd phrap_extras.tar.gz | tar xvf -
cp phrap_extras/* .
Compile gcphrap by typing
make gcphrap
Copy the newly created 'phrap' and 'gcphrap' executable files to /usr/software/phrap (use the version number of the file you have been sent):
sudo mkdir -p /usr/software/phrap/phrap_0.990329
sudo ln -s /usr/software/phrap/phrap_0.990329 /usr/software/phrap/phrap
sudo cp phrap /usr/software/phrap/phrap
sudo cp gcphrap /usr/software/phrap/phrap
sudo chmod go-r /usr/software/phrap/phrap/phrap
sudo chmod go-r /usr/software/phrap/phrap/gcphrap