Instructions to install SLAG
Download SLAGball.tgz from https://github.com/cfcrane/SLAG. It is currently available as release 1.0.0.
Run "md5sum SLAGball.tgz" and compare the result to the file SLAGballmd5sum.txt. Proceed if the checksums are identical.
Move SLAGball.tgz to the directory where you want to keep it.
Run "tar -xzf SLAGball.tgz" to expand the directory tree. Its root, slagbase, contains SLAG.pl, SLAG.sif, and
setupSLAGconfigurations.pl. SLAG.sif is a Singularity container that can run SLAG.pl. Subdirectory templates contains
24 templates for configuration files, which are the way to communicate file names and settings to SLAG.pl or SLAG.sif.
Subdirectory testcfg contains 24 populated configuration files and 24 shell scripts to validate a successful download
and function on your system. These shell scripts are meant to be executed from the testout subdirectory. For example,
running ../testcfg/runCNTLRcanuSLAGtest.sh tests the container-included canu assembler with a test database and test
query from subdirectory testdata, with output files going to testout. Success is indicated by the presence of filenames
with the suffix "subset.contigs" in testout or in a family of "*work" subdirectories of testout. Assemblers canu,
Unicycler, and SPAdes produce "*work" subdirectories that must be deleted if you want to repeat the test. The test
scripts and configuration files are named by the convention LR = long read (2000 - 6000 bases), SR = short read (2x150
bases), MR = medium read (200 - 600 bases), LR1 = long reads with single fragmentation, LR2 = long reads with double
(overlapping) fragmentation, PI = Racon polishing, CNT = invocation of SLAG.sif (the Singularity container), and the
assembler name. Each shell script should take a few minutes, except for the PI scripts, which take up to one hour.
The test query is phenylalanine ammonia lyase from maize, and the test reads are simulated based on the interval from
base 320000000 to base 330000000 in wheat cv. 'Chinese Spring' chromosome 6D. This interval contains one of the wheat
copies of the phenylalanine ammonia lyase gene.
If you are an administrator, you can add the path to slagbase to users' default $PATH, or include it in the set of
loadable modules.