Comments (2)
The functions can accept a tmp_dir parameter, they just currently aren't being passed one.
We'd have to track down each time these functions are called from QIIME and pass the temp_dir from the qiime_config when they are called rather then letting them default to the gettempdir value:
uclust_cluster_from_sorted_fasta_filepath
uclust_search_and_align_from_fasta_filepath
uclust_fasta_sort_from_filepath
from burrito-fillings.
A work-around until we have this in place will be to set the one of the three environment variables that python looks at when trying to determine the value for tempfile.tempdir (see here). These are:
TMPDIR
TEMP
TMP
Note that you may need to set this variable in ~/.bashrc
(not ~/.bash_profile
!) if the shell that will execute these jobs is not a login shell. This is likely the case if you're using QIIME's parallel wrappers. So, you'd want to do something like this:
echo "export TMPDIR=$HOME/temp" >> ~/.bashrc
from burrito-fillings.
Related Issues (20)
- brokit-wrapped applications that are not currently installed in the QIIME VM HOT 7
- missing tmp dir in get_clusters_from_fasta_filepath function from uclust
- Allow for `--usearch_local` in usearch 6.1 HOT 1
- update brokit license information to indicate that it's actually GPL HOT 1
- Vienna package controller
- brokit.get_clusters_from_fasta_filepath failing to remove output files HOT 1
- Change to the numpy doc standard for sortmerna + sumaclust api's
- add import of cogent aligner for access in QIIME
- update to use skbio 0.1.4
- updates for transition from skbio to burrito for application controller framework HOT 6
- usearch de novo (no chimera checking) gives incorrect results
- update to skbio 0.2.1
- change name of brokit and do a 0.1.0 release HOT 3
- burrito-fillings is missing __version__ HOT 4
- improve uclust application controller error reporting
- grep the burrito-fillings code base for /tmp and replace with tempfile.gettempdir()
- clean-up usage of "/tmp" for fillings most frequently used by QIIME HOT 2
- Mothur app controller fails when temp directory has dash in filepath
- update to swarm 2 HOT 1
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from burrito-fillings.