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miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
17 stars 23 forks source link

Conda install broken; cannot find python modules #27

Open lsmainzer opened 6 years ago

lsmainzer commented 6 years ago

Hey. While testing mirtop, I followed the suggested instructions using Conda. But mirtop is unable to find python modules:

mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam Traceback (most recent call last): File "Testing_mirtop/bin/mirtop", line 9, in load_entry_point('mirtop==0.1.8a', 'console_scripts', 'mirtop')() File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 560, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2648, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2302, in load File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2308, in resolve File "Testing_mirtop/mirtop/mirtop/command_line.py", line 7, in from mirtop.libs.simulator import simulate File "Testing_mirtop/mirtop/mirtop/libs/simulator.py", line 3, in from mirtop.libs.read import get_fasta File "Testing_mirtop/mirtop/mirtop/libs/read.py", line 8, in import pybedtools

lpantano commented 6 years ago

Hi,

Thanks for that, I would check the conda recipe to see if I forgot that dependency. It is weird because it is there in the recipe, so not sure why is not installing the tool.

Just to confirm, did you use?

Conda install -c bioconda mirtop

Thanks

On Jan 19, 2018, at 3:52 PM, lsmainzer notifications@github.com wrote:

Hey. While testing mirtop, I followed the suggested instructions using Conda. But mirtop is unable to find python modules:

mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam Traceback (most recent call last): File "Testing_mirtop/bin/mirtop", line 9, in load_entry_point('mirtop==0.1.8a', 'console_scripts', 'mirtop')() File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 560, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2648, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2302, in load File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2308, in resolve File "Testing_mirtop/mirtop/mirtop/command_line.py", line 7, in from mirtop.libs.simulator import simulate File "Testing_mirtop/mirtop/mirtop/libs/simulator.py", line 3, in from mirtop.libs.read import get_fasta File "Testing_mirtop/mirtop/mirtop/libs/read.py", line 8, in import pybedtools

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cjfields commented 6 years ago

This might be worth checking in w/ our sysadmins on the cluster, my guess is their version of conda may not allow user-based installs. If so we'll likely need to install a user- (or group-) specific conda setup.

Just checking, but should we focus on python 2 or 3 for miniconda?

lpantano commented 6 years ago

Hi!

Thanks for checking this!

For now, 2.7.

On Jan 22, 2018, at 10:36 AM, Chris Fields notifications@github.com wrote:

This might be worth checking in w/ our sysadmins on the cluster, my guess is their version of conda may not allow user-based installs. If so we'll likely need to install a user- (or group-) specific conda setup.

Just checking, but should we focus on python 2 or 3 for miniconda?

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