installation error - porechop
mjfi2sb3 opened this issue · 9 comments
mjfi2sb3 commented
Hi,
I am getting the following error related to porechop while compiling. Any suggestions how to resolve?
Processing dependencies for pomoxis==0.2.0 Searching for Porechop Reading https://pypi.org/simple/Porechop/ Couldn't find index page for 'Porechop' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.org/simple/ No local packages or working download links found for Porechop error: Could not find suitable distribution for Requirement.parse('Porechop') make: *** [install] Error 1
cjw85 commented
Hi @mjfi2sb3,
Can you provide the command you are running to install pomoxis? Porechop is indeed not available on pypi, though the installation methods in the README.md (bar the last one if run as-is), should not cause an attempt to be made.
If you are a conda user you will most likely wish to follow the instructions under "Installation with conda", if not the instructions under "Installation from source" will be more appropriate.
mjfi2sb3 commented
Hi @cjw85,
I actually tried "Installation with conda" (CONDA=/path/to/anaconda3 make
conda) and "Installation from source" (make install). Both gave the same
error.
Best,
/SB
…On Mon, 7 Jan 2019 at 11:59, cjw85 ***@***.***> wrote:
Hi @mjfi2sb3 <https://github.com/mjfi2sb3>,
Can you provide the command you are running to install pomoxis? Porechop
is indeed not available on pypi, though the installation methods in the
README.md (bar the last one if run as-is), should not cause an attempt to
be made.
If you are a conda user you will most likely wish to follow the
instructions under "Installation with conda", if not the instructions under
"Installation from source" will be more appropriate.
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cjw85 commented
The conda route would install Porechop using conda, so I am puzzled as to how you would get the above error message. Can you attach the full terminal output, perhaps something is going wrong earlier on?
mjfi2sb3 commented
Hi,
The command I run is
CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make install
and the log is attached.
Best & thanks,
/SB
…On Mon, 7 Jan 2019 at 12:08, cjw85 ***@***.***> wrote:
The conda route would install Porechop using conda, so I am puzzled as to
how you would get the above error message. Can you attach the full terminal
output, perhaps something is going wrong earlier on?
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cd submodules/bwapy && make bwa/libbwa.a
make[1]: Entering directory `/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/submodules/bwapy'
make[1]: `bwa/libbwa.a' is up to date.
make[1]: Leaving directory `/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/submodules/bwapy'
. ./venv/bin/activate && cd submodules/bwapy && python setup.py install
running install
running bdist_egg
running egg_info
writing bwapy.egg-info/PKG-INFO
writing dependency_links to bwapy.egg-info/dependency_links.txt
writing entry points to bwapy.egg-info/entry_points.txt
writing requirements to bwapy.egg-info/requires.txt
writing top-level names to bwapy.egg-info/top_level.txt
reading manifest file 'bwapy.egg-info/SOURCES.txt'
writing manifest file 'bwapy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bwapy
copying build/lib.linux-x86_64-3.7/bwapy/__init__.py -> build/bdist.linux-x86_64/egg/bwapy
copying build/lib.linux-x86_64-3.7/bwapy/libbwa.py -> build/bdist.linux-x86_64/egg/bwapy
copying build/lib.linux-x86_64-3.7/bwalib.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/bwapy/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/bwapy/libbwa.py to libbwa.cpython-37.pyc
creating stub loader for bwalib.cpython-37m-x86_64-linux-gnu.so
byte-compiling build/bdist.linux-x86_64/egg/bwalib.py to bwalib.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bwapy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
creating 'dist/bwapy-0.1.3-py3.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing bwapy-0.1.3-py3.7-linux-x86_64.egg
removing '/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg' (and everything under it)
creating /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg
Extracting bwapy-0.1.3-py3.7-linux-x86_64.egg to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages
bwapy 0.1.3 is already the active version in easy-install.pth
Installing bwamempy script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installed /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg
Processing dependencies for bwapy==0.1.3
Searching for cffi==1.11.5
Best match: cffi 1.11.5
Adding cffi 1.11.5 to easy-install.pth file
Using /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages
Searching for pycparser==2.19
Best match: pycparser 2.19
Adding pycparser 2.19 to easy-install.pth file
Using /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages
Finished processing dependencies for bwapy==0.1.3
. ./venv/bin/activate && POMO_BINARIES=1 python setup.py install
running install
running bdist_egg
running egg_info
writing pomoxis.egg-info/PKG-INFO
writing dependency_links to pomoxis.egg-info/dependency_links.txt
writing entry points to pomoxis.egg-info/entry_points.txt
writing requirements to pomoxis.egg-info/requires.txt
writing top-level names to pomoxis.egg-info/top_level.txt
reading manifest file 'pomoxis.egg-info/SOURCES.txt'
writing manifest file 'pomoxis.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pomoxis
copying build/lib/pomoxis/__init__.py -> build/bdist.linux-x86_64/egg/pomoxis
copying build/lib/pomoxis/watcher.py -> build/bdist.linux-x86_64/egg/pomoxis
creating build/bdist.linux-x86_64/egg/pomoxis/align
copying build/lib/pomoxis/align/__init__.py -> build/bdist.linux-x86_64/egg/pomoxis/align
copying build/lib/pomoxis/align/bwa.py -> build/bdist.linux-x86_64/egg/pomoxis/align
copying build/lib/pomoxis/align/common.py -> build/bdist.linux-x86_64/egg/pomoxis/align
copying build/lib/pomoxis/align/minimap.py -> build/bdist.linux-x86_64/egg/pomoxis/align
copying build/lib/pomoxis/align/py2client.py -> build/bdist.linux-x86_64/egg/pomoxis/align
creating build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/__init__.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/bio.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/catalogue_errors.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/common_errors_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/coverage_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/qscores_from_summary.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/ref_seqs_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/simulate_calls.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/stats_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/subsample_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/summary_from_stats.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/trim_alignments.py -> build/bdist.linux-x86_64/egg/pomoxis/common
copying build/lib/pomoxis/common/util.py -> build/bdist.linux-x86_64/egg/pomoxis/common
creating build/bdist.linux-x86_64/egg/pomoxis/provider
copying build/lib/pomoxis/provider/__init__.py -> build/bdist.linux-x86_64/egg/pomoxis/provider
copying build/lib/pomoxis/provider/replayfast5.py -> build/bdist.linux-x86_64/egg/pomoxis/provider
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/watcher.py to watcher.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/bwa.py to bwa.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/common.py to common.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/minimap.py to minimap.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/py2client.py to py2client.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/bio.py to bio.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/catalogue_errors.py to catalogue_errors.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/common_errors_from_bam.py to common_errors_from_bam.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/coverage_from_bam.py to coverage_from_bam.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/qscores_from_summary.py to qscores_from_summary.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/ref_seqs_from_bam.py to ref_seqs_from_bam.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/simulate_calls.py to simulate_calls.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/stats_from_bam.py to stats_from_bam.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/subsample_bam.py to subsample_bam.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/summary_from_stats.py to summary_from_stats.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/trim_alignments.py to trim_alignments.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/util.py to util.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/provider/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pomoxis/provider/replayfast5.py to replayfast5.cpython-37.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/exes
copying bincache/minimap2 -> build/bdist.linux-x86_64/egg/exes
copying bincache/miniasm -> build/bdist.linux-x86_64/egg/exes
copying bincache/racon -> build/bdist.linux-x86_64/egg/exes
copying bincache/samtools -> build/bdist.linux-x86_64/egg/exes
copying bincache/bcftools -> build/bdist.linux-x86_64/egg/exes
copying bincache/seqkit -> build/bdist.linux-x86_64/egg/exes
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/assess_assembly -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/intersect_assembly_errors -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/mini_align -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/mini_assemble -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/assess_assembly to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/intersect_assembly_errors to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/mini_align to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/mini_assemble to 755
copying pomoxis.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pomoxis.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pomoxis-0.2.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pomoxis-0.2.0-py3.7.egg
removing '/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg' (and everything under it)
creating /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg
Extracting pomoxis-0.2.0-py3.7.egg to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages
pomoxis 0.2.0 is already the active version in easy-install.pth
Installing assess_assembly script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing intersect_assembly_errors script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing mini_align script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing mini_assemble script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing align_serve script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing catalogue_errors script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing common_errors_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing coverage_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing coverage_from_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing fast_convert script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing long_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing pomoxis_path script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing qscores_from_summary script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing read_until_filter script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing ref_seqs_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing simulate_calls script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing split_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing stats_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing subsample_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing summary_from_stats script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installing trim_alignments script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin
Installed /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg
Processing dependencies for pomoxis==0.2.0
Searching for Porechop
Reading https://pypi.org/simple/Porechop/
File "build/bdist.linux-x86_64/egg/pomoxis/__init__.py", line 20
asyncio.async(wakeup())
^
SyntaxError: invalid syntax
File "build/bdist.linux-x86_64/egg/pomoxis/watcher.py", line 85
self._loop.call_soon_threadsafe(asyncio.async, self._process_file(event))
^
SyntaxError: invalid syntax
File "/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/__init__.py", line 20
asyncio.async(wakeup())
^
SyntaxError: invalid syntax
File "/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/watcher.py", line 85
self._loop.call_soon_threadsafe(asyncio.async, self._process_file(event))
^
SyntaxError: invalid syntax
Couldn't find index page for 'Porechop' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.org/simple/
No local packages or working download links found for Porechop
error: Could not find suitable distribution for Requirement.parse('Porechop')
make: *** [install] Error 1
cjw85 commented
I think the command you want to be running is:
CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make conda
(I can see there is a typo in the README which we will correct). You are using python3.7, with which we do not test; you can see some errors in the log which pertain to this, though I doubt they are the cause of the Porechop issue.
mjfi2sb3 commented
Hi,
It seems that you are right `CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make
conda` is the command I should have used (see attached log). However, when
I run some of the commands such as trim_alignments -h I get the
following error. Is this due to the python version?
`
trim_alignments -h
Traceback (most recent call last):
File "/bcl-nas/apps/anaconda3/v2018.12/bin/trim_alignments", line 11, in
<module>
load_entry_point('pomoxis==0.2.0', 'console_scripts',
'trim_alignments')()
File
"/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 487, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2728, in load_entry_point
return ep.load()
File
"/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2346, in load
return self.resolve()
File
"/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2352, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File
"/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/__init__.py",
line 20
asyncio.async(wakeup())
^
SyntaxError: invalid syntax
`
Best,
/SB
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CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make conda
. /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda remove -n pomoxis --all
Remove all packages in environment /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis:
## Package Plan ##
environment location: /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis
The following packages will be REMOVED:
bcftools: 1.7-0 bioconda
bzip2: 1.0.6-h470a237_2 conda-forge
ca-certificates: 2018.11.29-ha4d7672_0 conda-forge
certifi: 2018.11.29-py36_1000 conda-forge
curl: 7.63.0-h74213dd_0 conda-forge
krb5: 1.16.2-hbb41f41_0 conda-forge
libcurl: 7.63.0-hbdb9355_0 conda-forge
libdeflate: 1.0-h470a237_0 bioconda
libedit: 3.1.20170329-0 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc: 7.2.0-h69d50b8_2 conda-forge
libgcc-ng: 8.2.0-hdf63c60_1
libssh2: 1.8.0-h5b517e9_3 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
miniasm: 0.3_r179-ha92aebf_0 bioconda
minimap2: 2.14-ha92aebf_0 bioconda
ncurses: 5.9-10 conda-forge
openssl: 1.0.2p-h470a237_2 conda-forge
pigz: 2.3.4-0 conda-forge
pip: 18.1-py36_1000 conda-forge
porechop: 0.2.3_seqan2.1.1-py36h2d50403_3 bioconda
python: 3.6.6-h5001a0f_3 conda-forge
racon: 1.3.1-he941832_5 bioconda
readline: 7.0-0 conda-forge
samtools: 1.8-h46bd0b3_5 bioconda
seqkit: 0.8.0-2 bioconda
setuptools: 40.6.3-py36_0 conda-forge
sqlite: 3.26.0-h7b6447c_0
tk: 8.6.9-ha92aebf_0 conda-forge
wheel: 0.32.3-py36_0 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Proceed ([y]/n)? y
. /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda create -y -n pomoxis -c bioconda -c conda-forge porechop \
samtools=1.8 bcftools=1.7 seqkit=0.8.0 \
miniasm=0.3 minimap2=2.14 racon=1.3.1 \
python=3.6
Solving environment: done
## Package Plan ##
environment location: /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis
added / updated specs:
- bcftools=1.7
- miniasm=0.3
- minimap2=2.14
- porechop
- python=3.6
- racon=1.3.1
- samtools=1.8
- seqkit=0.8.0
The following NEW packages will be INSTALLED:
bcftools: 1.7-0 bioconda
bzip2: 1.0.6-h470a237_2 conda-forge
ca-certificates: 2018.11.29-ha4d7672_0 conda-forge
certifi: 2018.11.29-py36_1000 conda-forge
curl: 7.63.0-h74213dd_0 conda-forge
krb5: 1.16.2-hbb41f41_0 conda-forge
libcurl: 7.63.0-hbdb9355_0 conda-forge
libdeflate: 1.0-h470a237_0 bioconda
libedit: 3.1.20170329-0 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc: 7.2.0-h69d50b8_2 conda-forge
libgcc-ng: 8.2.0-hdf63c60_1
libssh2: 1.8.0-h5b517e9_3 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
miniasm: 0.3_r179-ha92aebf_0 bioconda
minimap2: 2.14-ha92aebf_0 bioconda
ncurses: 5.9-10 conda-forge
openssl: 1.0.2p-h470a237_2 conda-forge
pigz: 2.3.4-0 conda-forge
pip: 18.1-py36_1000 conda-forge
porechop: 0.2.3_seqan2.1.1-py36h2d50403_3 bioconda
python: 3.6.6-h5001a0f_3 conda-forge
racon: 1.3.1-he941832_5 bioconda
readline: 7.0-0 conda-forge
samtools: 1.8-h46bd0b3_5 bioconda
seqkit: 0.8.0-2 bioconda
setuptools: 40.6.3-py36_0 conda-forge
sqlite: 3.26.0-h7b6447c_0
tk: 8.6.9-ha92aebf_0 conda-forge
wheel: 0.32.3-py36_0 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate pomoxis
#
# To deactivate an active environment, use
#
# $ conda deactivate
grep -v Porechop requirements.txt > conda_reqs.txt
. /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda activate pomoxis && pip install -r conda_reqs.txt
Collecting aiozmq (from -r conda_reqs.txt (line 3))
Using cached https://files.pythonhosted.org/packages/c8/5b/4ce8584fcd676664ba43170d9871ae177837fa72f59c08766bc0c589e177/aiozmq-0.7.1-py3-none-any.whl
Collecting biopython>=1.63 (from -r conda_reqs.txt (line 4))
Using cached https://files.pythonhosted.org/packages/28/15/8ac646ff24cfa2588b4d5e5ea51e8d13f3d35806bd9498fbf40ef79026fd/biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl
Collecting cffi (from -r conda_reqs.txt (line 5))
Using cached https://files.pythonhosted.org/packages/6d/c0/47db8f624f3e4e2f3f27be03a93379d1ba16a1450a7b1aacfa0366e2c0dd/cffi-1.11.5-cp36-cp36m-manylinux1_x86_64.whl
Collecting fast5_research (from -r conda_reqs.txt (line 6))
Collecting intervaltree (from -r conda_reqs.txt (line 7))
Collecting matplotlib (from -r conda_reqs.txt (line 8))
Using cached https://files.pythonhosted.org/packages/71/07/16d781df15be30df4acfd536c479268f1208b2dfbc91e9ca5d92c9caf673/matplotlib-3.0.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting mappy (from -r conda_reqs.txt (line 9))
Collecting msgpack-python (from -r conda_reqs.txt (line 10))
Collecting numpy (from -r conda_reqs.txt (line 11))
Using cached https://files.pythonhosted.org/packages/ff/7f/9d804d2348471c67a7d8b5f84f9bc59fd1cefa148986f2b74552f8573555/numpy-1.15.4-cp36-cp36m-manylinux1_x86_64.whl
Collecting pandas (from -r conda_reqs.txt (line 12))
Using cached https://files.pythonhosted.org/packages/e1/d8/feeb346d41f181e83fba45224ab14a8d8af019b48af742e047f3845d8cff/pandas-0.23.4-cp36-cp36m-manylinux1_x86_64.whl
Collecting pysam (from -r conda_reqs.txt (line 13))
Using cached https://files.pythonhosted.org/packages/6f/f4/e12faf1618e977a868fe66d40288fc3dd989a10cc4c77603da33a7634a18/pysam-0.15.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting scrappie (from -r conda_reqs.txt (line 14))
Using cached https://files.pythonhosted.org/packages/9a/45/0c0d7a1ecf056518aa63e6590ef83ed8daefaab9bae27694df2482536185/scrappie-1.4.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting watchdog (from -r conda_reqs.txt (line 15))
Collecting pyzmq>=13.1 (from aiozmq->-r conda_reqs.txt (line 3))
Using cached https://files.pythonhosted.org/packages/48/93/59592cb294761aaa40589b544eaa5175446d687ff95beeeb666de60f3274/pyzmq-17.1.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting pycparser (from cffi->-r conda_reqs.txt (line 5))
Collecting progressbar2 (from fast5_research->-r conda_reqs.txt (line 6))
Using cached https://files.pythonhosted.org/packages/0c/78/0ae9129f12098adbcfee0c51a81dfa94cdc1853142aa4d62e63c6a355bd7/progressbar2-3.39.2-py2.py3-none-any.whl
Collecting h5py (from fast5_research->-r conda_reqs.txt (line 6))
Using cached https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting sortedcontainers<3.0,>=2.0 (from intervaltree->-r conda_reqs.txt (line 7))
Using cached https://files.pythonhosted.org/packages/13/f3/cf85f7c3a2dbd1a515d51e1f1676d971abe41bba6f4ab5443240d9a78e5b/sortedcontainers-2.1.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.1 (from matplotlib->-r conda_reqs.txt (line 8))
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib->-r conda_reqs.txt (line 8))
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->-r conda_reqs.txt (line 8))
Using cached https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->-r conda_reqs.txt (line 8))
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas->-r conda_reqs.txt (line 12))
Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB)
100% |████████████████████████████████| 512kB 2.8MB/s
Collecting argh>=0.24.1 (from watchdog->-r conda_reqs.txt (line 15))
Using cached https://files.pythonhosted.org/packages/06/1c/e667a7126f0b84aaa1c56844337bf0ac12445d1beb9c8a6199a7314944bf/argh-0.26.2-py2.py3-none-any.whl
Collecting pathtools>=0.1.1 (from watchdog->-r conda_reqs.txt (line 15))
Collecting PyYAML>=3.10 (from watchdog->-r conda_reqs.txt (line 15))
Collecting python-utils>=2.3.0 (from progressbar2->fast5_research->-r conda_reqs.txt (line 6))
Using cached https://files.pythonhosted.org/packages/eb/a0/19119d8b7c05be49baf6c593f11c432d571b70d805f2fe94c0585e55e4c8/python_utils-2.3.0-py2.py3-none-any.whl
Collecting six (from progressbar2->fast5_research->-r conda_reqs.txt (line 6))
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->-r conda_reqs.txt (line 8)) (40.6.3)
Installing collected packages: pyzmq, aiozmq, numpy, biopython, pycparser, cffi, six, python-utils, progressbar2, h5py, fast5-research, sortedcontainers, intervaltree, python-dateutil, cycler, kiwisolver, pyparsing, matplotlib, mappy, msgpack-python, pytz, pandas, pysam, scrappie, argh, pathtools, PyYAML, watchdog
Successfully installed PyYAML-3.13 aiozmq-0.7.1 argh-0.26.2 biopython-1.73 cffi-1.11.5 cycler-0.10.0 fast5-research-1.2.8 h5py-2.9.0 intervaltree-3.0.2 kiwisolver-1.0.1 mappy-2.14 matplotlib-3.0.2 msgpack-python-0.5.6 numpy-1.15.4 pandas-0.23.4 pathtools-0.1.2 progressbar2-3.39.2 pycparser-2.19 pyparsing-2.3.0 pysam-0.15.1 python-dateutil-2.7.5 python-utils-2.3.0 pytz-2018.9 pyzmq-17.1.2 scrappie-1.4.1 six-1.12.0 sortedcontainers-2.1.0 watchdog-0.9.0
. /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda activate pomoxis && python setup.py install \
--single-version-externally-managed --record=conda_install.out
running install
running build
running build_py
running build_scripts
running install_lib
creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis
copying build/lib/pomoxis/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis
copying build/lib/pomoxis/watcher.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis
creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
copying build/lib/pomoxis/align/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
copying build/lib/pomoxis/align/bwa.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
copying build/lib/pomoxis/align/common.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
copying build/lib/pomoxis/align/minimap.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
copying build/lib/pomoxis/align/py2client.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align
creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/bio.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/catalogue_errors.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/common_errors_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/coverage_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/qscores_from_summary.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/ref_seqs_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/simulate_calls.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/stats_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/subsample_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/summary_from_stats.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/trim_alignments.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
copying build/lib/pomoxis/common/util.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common
creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider
copying build/lib/pomoxis/provider/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider
copying build/lib/pomoxis/provider/replayfast5.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/__init__.py to __init__.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/watcher.py to watcher.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/__init__.py to __init__.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/bwa.py to bwa.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/common.py to common.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/minimap.py to minimap.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/py2client.py to py2client.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/__init__.py to __init__.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/bio.py to bio.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/catalogue_errors.py to catalogue_errors.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/common_errors_from_bam.py to common_errors_from_bam.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/coverage_from_bam.py to coverage_from_bam.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/qscores_from_summary.py to qscores_from_summary.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/ref_seqs_from_bam.py to ref_seqs_from_bam.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/simulate_calls.py to simulate_calls.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/stats_from_bam.py to stats_from_bam.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/subsample_bam.py to subsample_bam.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/summary_from_stats.py to summary_from_stats.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/trim_alignments.py to trim_alignments.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/util.py to util.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider/__init__.py to __init__.cpython-36.pyc
byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider/replayfast5.py to replayfast5.cpython-36.pyc
running install_egg_info
running egg_info
writing pomoxis.egg-info/PKG-INFO
writing dependency_links to pomoxis.egg-info/dependency_links.txt
writing entry points to pomoxis.egg-info/entry_points.txt
writing requirements to pomoxis.egg-info/requires.txt
writing top-level names to pomoxis.egg-info/top_level.txt
reading manifest file 'pomoxis.egg-info/SOURCES.txt'
writing manifest file 'pomoxis.egg-info/SOURCES.txt'
Copying pomoxis.egg-info to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis-0.2.0-py3.6.egg-info
running install_scripts
copying build/scripts-3.6/assess_assembly -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
copying build/scripts-3.6/intersect_assembly_errors -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
copying build/scripts-3.6/mini_align -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
copying build/scripts-3.6/mini_assemble -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/assess_assembly to 755
changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/intersect_assembly_errors to 755
changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/mini_align to 755
changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/mini_assemble to 755
Installing align_serve script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing catalogue_errors script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing common_errors_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing coverage_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing coverage_from_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing fast_convert script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing long_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing pomoxis_path script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing qscores_from_summary script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing read_until_filter script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing ref_seqs_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing simulate_calls script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing split_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing stats_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing subsample_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing summary_from_stats script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
Installing trim_alignments script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin
writing list of installed files to 'conda_install.out'
rm conda_reqs.txt
cjw85 commented
I believe this is an issue with using python 3.7: a quick look at the python 3.7 release notes tells me async and await are now reserved keywords, so the above code is not valid python 3.7.
As such pomoxis is not compatible with python 3.7 (and isnt likely to be made so in the immediate future).
mjfi2sb3 commented
Hi @cjw85;
yes, I created a virtual environment for python 3.6 under anaconda (*conda
create -n py36 python=3.6 anaconda*) then installed pomoxis in this
environment as you described
(*CONDA=/bcl-nas/apps/anaconda3/v2018.12_02/envs/py36/
make conda*). This seems to have solved the problem and all tools seem to
work including those that call porechop.
Best & thanks again.
/SB
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cjw85 commented
Thanks for confirming everything is now working.