issue with Ruffus 2.8.1 and gevent library not present (ant-login)

[webermarcolivier]

Important Note: I had to downgrade from ruffus 2.8.1 to 2.6.3 because of bad handling of the gevent library. Running the pipeline on the cluster environment, I kept getting the following error:

Original exception:

    Exception #1
      'builtins.NameError(name 'gevent' is not defined)' raised in ...
       Task = def filter_alignments(...):
       Job  = [Task04_convert_sam_to_bam/WT_R2_16424_ACTTGA_sorted.bam -> [Task05_filter_alignments/WT_R2_16424_ACTTGA.filtered.bed, Task05_filter_alignments/WT_R2_16424_ACTTGA.filtered.bed.nreads], WT_R2_16424_ACTTGA, Task04_convert_sam_to_bam, Task05_filter_alignments, filter_alignments, <LoggingProxy>, <unlocked _thread.lock>]
    
    Traceback (most recent call last):
      File "/nfs/users/lserrano/mweber/Software/python/envs/.virtualenvs/python351/lib/python3.5/site-packages/ruffus/task.py", line 712, in run_pooled_job_without_exceptions
        register_cleanup, touch_files_only)
      File "/nfs/users/lserrano/mweber/Software/python/envs/.virtualenvs/python351/lib/python3.5/site-packages/ruffus/task.py", line 544, in job_wrapper_io_files
        ret_val = user_defined_work_func(*params)
      File "/users/lserrano/mweber/bin/roesti/pipeline_roesti", line 1101, in filter_alignments
        job_other_options=job_other_options, retain_job_scripts=False)
      File "/nfs/users/lserrano/mweber/Software/python/envs/.virtualenvs/python351/lib/python3.5/site-packages/ruffus/drmaa_wrapper.py", line 581, in run_job
        verbose, resubmit, pipeline)
      File "/nfs/users/lserrano/mweber/Software/python/envs/.virtualenvs/python351/lib/python3.5/site-packages/ruffus/drmaa_wrapper.py", line 350, in run_job_using_drmaa
        cmd_str, drmaa_session, job_template, logger, pipeline)
      File "/nfs/users/lserrano/mweber/Software/python/envs/.virtualenvs/python351/lib/python3.5/site-packages/ruffus/drmaa_wrapper.py", line 239, in submit_drmaa_job
        gevent.sleep(GEVENT_TIMEOUT_STARTUP)
    NameError: name 'gevent' is not defined

I don't know why but ruffus 2.8.1 seems to have implemented the optional gevent package. In the drmaa_wrapper.py file, the presence of the library is first test,

try:
    import gevent
    HAVE_GEVENT = True
except ImportError:
    HAVE_GEVENT = False

but afterwards a simple try statement is not catching correclty the NameError exception, in function submit_drmaa_job:

try:
        gevent.sleep(GEVENT_TIMEOUT_STARTUP)
except JobSignalledBreak:
        # ...

[webermarcolivier]

fixed by installing package gevent,

conda install gevent