soedinglab
commands for splitfasta.pl do not work on conda installs
Expected Behavior
For the command splitfasta.pl ManyProteins.fasta to produce individual fastas like in the user guide.
Current Behavior
output from splitfasta.pl <filename>.fasta is splitfasta.pl: command not found
Context
My install steps:
$ conda install -c conda-forge -c bioconda hhsuite
$ git clone https://github.com/soedinglab/pdbx.git
$ cd pdbx
$ mkdir build
$ cd build
$ cmake -DUserInstallOption=ON ../
$ make install
$ mkdir ~/databases/hhsuite_dbs
$ cd ~/databases/hhsuite_dbs
$ wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/uniprot20_2013_03.tar.gz
$ tar -xvzf uniprot20_2013_03.tar.gz
Your Environment
Include as many relevant details about the environment you experienced the issue in.
- Version/Git commit used: 80a2ac3
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory): Intel
- Operating system and version: Linux, Ubuntu release 20.04.2 LTS
Most of the content of the scripts folder is unsupported (except I guess reformat.pl since that is pretty important) currently. We don't have the resources to maintain those :/
Two years later (v. 3.3.0): the scripts directory is available in the conda environment but the scripts are not in the $PATH, so one has to use them as $CONDA_PREFIX/scripts/splitfasta.pl. I think there is no reason not to add the scripts to the environment's $PATH.
