Public bug reported:
Take the simplest Snakefile possible:
```
rule test:
shell:
'echo Hello'
```
Running snakemake on this file fails with error message:
GLPSOL--GLPK LP/MIP Solver 5.0
Parameter(s) specified in the command line:
--cpxlp /tmp/11746-pulp.lp -o /tmp/11746-pulp.sol
Reading problem data from '/tmp/11746-pulp.lp'...
/tmp/11746-pulp.lp:5: missing constraint sense
CPLEX LP file processing error
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/snakemake/__init__.py", line 643, in
snakemake
success = workflow.execute(
File "/usr/lib/python3/dist-packages/snakemake/workflow.py", line 961, in
execute
success = scheduler.schedule()
File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 406, in
schedule
else self.job_selector_ilp(needrun)
File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 624, in
job_selector_ilp
prob.solve()
File "/usr/lib/python3/dist-packages/pulp/pulp.py", line 1643, in solve
status = solver.actualSolve(self, **kwargs)
File "/usr/lib/python3/dist-packages/pulp/solvers.py", line 380, in
actualSolve
raise PulpSolverError("PuLP: Error while executing "+self.path)
pulp.solvers.PulpSolverError: PuLP: Error while executing glpsol
A workaround is to uninstall the package glpk-utils.
ProblemType: Bug
DistroRelease: Ubuntu 21.04
Package: snakemake 5.24.1-2
ProcVersionSignature: Ubuntu 5.11.0-17.18-generic 5.11.12
Uname: Linux 5.11.0-17-generic x86_64
NonfreeKernelModules: wl
ApportVersion: 2.20.11-0ubuntu65
Architecture: amd64
CasperMD5CheckResult: unknown
CurrentDesktop: ubuntu:GNOME
Date: Wed May 19 14:25:48 2021
InstallationDate: Installed on 2021-01-19 (119 days ago)
InstallationMedia: Ubuntu 20.10 "Groovy Gorilla" - Release amd64 (20201022)
PackageArchitecture: all
SourcePackage: snakemake
UpgradeStatus: Upgraded to hirsute on 2021-04-27 (22 days ago)
** Affects: snakemake (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug hirsute wayland-session
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https://bugs.launchpad.net/bugs/1928940
Title:
snakemake fails with glpk-utils installed
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