Conda Install

[JChristopherEllis]

Installed Midas with the conda install and also download the database.

However, I get the following error....

Error: File not found: hs-blastn

Are there other items that need to be installed with conda?

Thanks, Chris

[nick-youngblut]

I ran into this too. It seems to be due to midas assuming that the executables are in certain paths instead of just checking the PATH var:

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'])

        for arg in ['hs-blastn', 'stream_seqs', 'bowtie2-build', 'bowtie2', 'samtools']:
                if not os.path.isfile(args[arg]):
                        sys.exit("\nError: File not found: %s\n" % args[arg])

        for arg in ['hs-blastn', 'bowtie2-build', 'bowtie2', 'samtools']:
                if not os.access(args[arg], os.X_OK):
                        sys.exit("\nError: File not executable: %s\n" % args[arg])

Changing this to:

from distutils.spawn import find_executable
for exe in [...]:
    if find_executable(exe) is None:
        sys.exit("\nError: File not found: {}\n".format(exe))

...would fix that check, but then the code that specifies the paths for the executables would also need to change. I'll create a PR

[marcomeola]

Can you specify which file has to be modified?

[nick-youngblut]

Can you specify which file has to be modified?

./midas/utility.py

[npavlovikj]

Any updates on merging Nick's PR? I can patch the conda recipe to look for the executables in PATH, but it is much better if the code is updated in MIDAS release itself.

[cirodri1]

Hello! I am encountering the same issue, but since I am using a High Performance Computing cluster from my institution I do not have the permissions to change the files. Has this been solved in any other way or with an update? The version that is installed in the HPC is midas/1.3.2