Conda install broken; cannot find python modules

[lsmainzer]

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]

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

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On Jan 19, 2018, at 3:52 PM, lsmainzer ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#27>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HPxleHNRnHzocBFmmSnTYV6rPqvjks5tMQCDgaJpZM4RlCOQ>.

[cjfields]

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]

Hi! Thanks for checking this! For now, 2.7.

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On Jan 22, 2018, at 10:36 AM, Chris Fields ***@***.***> 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? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HMbKk-jtV6iu0YOsKBmBhBh5lXCcks5tNKsHgaJpZM4RlCOQ>.