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I have MIDAS installed and all of the 3rd party tools as well. Has anyone else had this issue?
(midas_env) -bash-4.1$ which run_midas.py /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/midas_env/bin/run_midas.py (midas_env) -bash-4.1$ which hs-blastn /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/midas_env/bin/hs-blastn (midas_env) -bash-4.1$ run_midas.py species -1 WATER-17B_P01-CTRL_BC-80_BR-2_S80_001.paired_trimmed.fna -t 4 tmp_output Error: File not found: hs-blastn
From this https://github.com/snayfach/MIDAS/blame/master/midas/utility.py
def add_executables(args): """ Identify relative file and directory paths """ src_dir = os.path.dirname(os.path.abspath(__file__)) main_dir = os.path.dirname(src_dir) args['stream_seqs'] = '/'.join([src_dir, 'run', 'stream_seqs.py']) args['hs-blastn'] = '/'.join([main_dir, 'bin', platform.system(), 'hs-blastn']) args['bowtie2-build'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2-build']) args['bowtie2'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2']) args['samtools'] = '/'.join([main_dir, 'bin', platform.system(), 'samtools'])
What about using this instead as default? https://codereview.stackexchange.com/questions/123597/find-a-specific-file-or-find-all-executable-files-within-the-system-path
The text was updated successfully, but these errors were encountered:
I ended up doing this for the python2 installation b/c the python3 version had an io error with the TextIOWrapper in the snps module:
io
TextIOWrapper
snps
conda create --name midas2_env -c bioconda python=2.7 --yes
Then I changed this file:
nano /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/midas2_env/lib/python2.7/site-packages/midas/utility.py
to the following:
def add_executables(args): """ Identify relative file and directory paths """ src_dir = os.path.dirname(os.path.abspath(__file__)) main_dir = os.path.dirname(src_dir) bin_dir = "/" + os.path.join(*sys.executable.split("/")[:-1]) args['stream_seqs'] = '/'.join([src_dir, 'run', 'stream_seqs.py']) args['hs-blastn'] = '/'.join([bin_dir, 'hs-blastn']) args['bowtie2-build'] = '/'.join([bin_dir, 'bowtie2-build']) args['bowtie2'] = '/'.join([bin_dir, 'bowtie2']) args['samtools'] = '/'.join([bin_dir, 'samtools'])
Sorry, something went wrong.
If anyone needs this:
pip install git+https://github.com/jolespin/MIDAS
No branches or pull requests
I have MIDAS installed and all of the 3rd party tools as well. Has anyone else had this issue?
From this https://github.com/snayfach/MIDAS/blame/master/midas/utility.py
What about using this instead as default?
https://codereview.stackexchange.com/questions/123597/find-a-specific-file-or-find-all-executable-files-within-the-system-path
The text was updated successfully, but these errors were encountered: