pmfe-subopt

[spoznan]

With the recent changes /projects/rna/PMFEUpdated-2020.09.10-MDS-mschmidt34/GTDMMBSoftware2020/pmfe/bin doesn't contain pmfe-subopt. How can we run pmfe-subopt?

[maxieds]

@spoznan
Thank you for bringing this issue to my attention!

There were a few typos in the CMakeLists.txt build file that is newer as of pull request #26. This is how I built the binaries the last time I checked in on math-mulberry. After I corrected this problem with a new commit filed under that PR, the requested binaries you expected are now there.

In general, however, please be advised that I intended everything to get run from within the wrapper script (now renamed). The usage is as follows:

$ ./PMFECommandRunner.sh pmfe-subopt
 [PMFE-WRAPPER-SCRIPT] PMFE utilities compiled at 2020-12-15
 [PMFE-WRAPPER-SCRIPT] from GitHub commit 50ee218a7860762061eee35b235fbd77b0ea076f
 [PMFE-WRAPPER-SCRIPT] posted at 2020-10-06

Options:
  --sequence arg                 Sequence file
  -v [ --verbose ]               Write verbose debugging output
  -o [ --outfile ] arg           Output file
  --delta arg (=0)               Energy delta value
  -a [ --multiloop-penalty ] arg Multiloop penalty parameter
  -b [ --unpaired-penalty ] arg  Unpaired base penalty parameter
  -c [ --branch-penalty ] arg    Branching helix penalty parameter
  -d [ --dummy-scaling ] arg     Dummy scaling parameter
  -m [ --dangle-model ] arg (=1) Dangle model
  -s [ --sorted ]                Sort results in increasing energy order
  -t [ --num-threads ] arg (=0)  Number of threads
  -h [ --help ]                  Display this help message

Please close the issue when you are able to run the command. Otherwise let me know if you encounter any further runtime issues following the transition to the new build procedure.

--Maxie