FINDING SOFTWARE THAT IS NOT UNDER CONDA
If you can not find software under CONDA environments, you could check in these places before to ask for an install:
/opt/perun/bin/ **Note: ** Some software here may be available directly in the environmental path, so it'll show up when you type: which software_name in the command line
/scratch2/software/
if you are a fan of iqtree:
There are several versions of the program and you should use the specific builds for perun, it currently has installed versions:
1.6.1 (/opt/perun/bin/iqtree-1.6.1-intel) 1.5.5 (/opt/perun/bin/iqtree-omp-1.5.5-intel-build) these are builds that take advantage of the architecture of the cluster and perform task faster the the other executables in any other directory
if you use 1.5.5 then set this in your shell script source /scratch2/software/intel-build-2017/set-path
if you are fan of BLAST or PLAST
Blast and Plast use ncbi V4 formated databases: these must have been built with the flags -parse_seqids -hash_index):
To know the paths of the most updated databases for programs in this snippet click databases_locations
1- the most updated version of BLAST in under conda
2- the most updated version of PLAST is available directly in the environmental path
if you are fan of BLAT or LAST
1- BLAT is available directly in the environmental path. To use it, you have to build a database. The simplest way is by typing this command:
faToTwoBit in.fa out.2bit , where in.fa is your database_fastafile and out.2bit is the output_name then run the program: blat out.2but query_file -out=pslx [options] outputname.pslx
2- LAST is available at /scratch2/software/last-941/bin/
Build a lastable database: lastdb [options] output-name fasta-sequence-file(s) then you are golden to use the executable that suits your needs
if you are fan of DIAMOND/ac-DIAMOND, centrifuge or kraken-HLL
All of these programs are under their own conda environment.
To know the paths of the most updated databases for programs in this snippet click databases_locations