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Conda install broken; cannot find python modules #27
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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 ***@***.***> 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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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? |
Hi!
Thanks for checking this!
For now, 2.7.
… 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?
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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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