patch pymummer recipe

[rpetit3]

pymummer makes use of tempfile.mkdtemp() but specifies where the temp directory is made. Which does not play well with containers:

Traceback (most recent call last):
  File "/usr/local/bin/seroba", line 88, in <module>
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/seroba/tasks/sero_run.py", line 19, in run
    sero.run()
  File "/usr/local/lib/python3.8/site-packages/seroba/serotyping.py", line 481, in run
    self._prediction(assemblie_file,cluster)
  File "/usr/local/lib/python3.8/site-packages/seroba/serotyping.py", line 452, in _prediction
    self.sero, self.imp = Serotyping._find_serotype(assemblie_file,serogroup_fasta,self.meta_data_dict[serogroup],\
  File "/usr/local/lib/python3.8/site-packages/seroba/serotyping.py", line 261, in _find_serotype
    pymummer.nucmer.Runner(
  File "/usr/local/lib/python3.8/site-packages/pymummer/nucmer.py", line 139, in run
    tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.', dir=os.getcwd())
  File "/usr/local/lib/python3.8/tempfile.py", line 358, in mkdtemp
    _os.mkdir(file, 0o700)
PermissionError: [Errno 13] Permission denied: '/tmp.run_nucmer.727hfrey'

This PR allows tempfile to figure out where to make the temp dir (see https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir)

Python searches a standard list of directories to find one which the calling user can create files in. The list is:

The directory named by the TMPDIR environment variable.
The directory named by the TEMP environment variable.
The directory named by the TMP environment variable.
A platform-specific location:
    - On Windows, the directories C:\TEMP, C:\TMP, \TEMP, and \TMP, in that order
    - On all other platforms, the directories /tmp, /var/tmp, and /usr/tmp, in that order.

As a last resort, the current working directory.

An upstream pull request has been submitted to pymummer (sanger-pathogens/pymummer#36), but a timeline of review is not available

This is also related to #35378

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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	pymummer-0.11.0-pyhdfd78af_1.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

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Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
pymummer	0.11.0--pyhdfd78af_1	show gzip -dc LinuxArtifacts/images/pymummer:0.11.0--pyhdfd78af_1.tar.gz | docker load

[rpetit3]

Testing

mamba create -n test-pymummer -c conda-forge -c bioconda 'python>3' 'pyfastaq>=3.10' mummer
conda activate test-pymummer
conda install LinuxArtifacts/packages/noarch/pymummer-0.11.0-pyhdfd78af_1.tar.bz2

# Looks good
grep mkdtemp /home/robert_petit/miniconda3/envs/test-pymummer/lib/python3.10/site-packages/pymummer/nucmer.py
        tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.')
        
# manually edited to print the tmpdir
export TMP=${PWD}/temptest
echo $TMP
/home/robert_petit/temp/test-pymummer/temptest

# test in python
python
>>> import pymummer
>>> test = pymummer.nucmer.Runner('x', 'y', 'z')
>>> test.run()
/home/robert_petit/temp/test-pymummer/temptest/tmp.run_nucmer.9coo3_6g

Much better this is now allowing tempfile to select the temp directory based on the user's environment and/or system

[rpetit3]

@BiocondaBot please add label

[mfansler]

Makes sense.

[mfansler]

@bioconda-bot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[rpetit3]

Thank you!