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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Circlator #106

Closed cchauve closed 2 years ago

cchauve commented 2 years ago

Circlator is not listed in the list of dependencies and nt installed by pip3, but when trying to run mob_recon, without the -c option, I get the error message ERROR:root:ERROR: Missing program: circlator ERROR:root:Error, you are missing needed programs for mob-suite, please install them and retry

kbessonov1984 commented 2 years ago

Hi Cederic, Which version of MOB-Suite are you using? The circlator dependency was removed on Dec 11, 2019 since installation of this dependency was problematic and not compatible with latest conda recipe. The circlator is still available in and its recipe and dependencies could be found here but I remember we had issue installing amos dependency. Try using the most recent version 3.0.3. This functionality was replaced by class detectCircularity.

If you still need to run previous version, we recommend the Singularity container where this dependency is already installed preserving the historical integrity. The list of possible images and instructions is available at https://biocontainers.pro/tools/mob_suite

cchauve commented 2 years ago

Thank you.

A stupid question then: how do I chose, using pip3, version 3.0.3 after I cloned thre github repo?

cedric

From: Kirill Bessonov @.***> Sent: May 3, 2022 12:16 To: phac-nml/mob-suite Cc: Computational Methods for Comparative Genomics at Simon Fraser University; Author Subject: Re: [phac-nml/mob-suite] Circlator (Issue #106)

Hi Cederic, Which version of MOB-Suite are you using? The circlator dependency was removedhttps://github.com/phac-nml/mob-suite/commit/da8dcd53ae72159c27ac7efae552bdee1cb66eb8 on Dec 11, 2019 since installation of this dependency was problematic and not compatible with latest conda recipe. Try using the most recent version 3.0.3. This functionality was replaced by class detectCircularityhttps://github.com/phac-nml/mob-suite/blob/39317225fcbd0a98fd1f1bd663d91932ae0fae8e/mob_suite/wrappers/__init__.py#L70

— Reply to this email directly, view it on GitHubhttps://github.com/phac-nml/mob-suite/issues/106#issuecomment-1116451648, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACXV7DVPDW2TQWXUXWWZSATVIFZEHANCNFSM5UUCYKWQ. You are receiving this because you authored the thread.Message ID: @.***>

kbessonov1984 commented 2 years ago

I would just run pip3 install --ignore-installed --force-reinstall mob-suite==3.0.3. This way if there are any residual temporary packages, the install will overwrite them mimicking a fresh install. If installing via pip3 you would need to manually install dependencies (mash and blast+). If running Ubuntu they can be installed via apt install mash ncbi-blast+ -y. Here is a docker file that lists all install commands from scratch on clean Linux system https://github.com/phac-nml/mob-suite/blob/master/mob_suite/docker/Dockerfile.

cchauve commented 2 years ago

Sorry to bug you again, but that does not work:

@.*** mob-suite > pip3 install --ignore-installed --force-reinstall mob-suite==3.0.3 Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic ERROR: Could not find a version that satisfies the requirement mob-suite==3.0.3 (from versions: 1.1, 1.2, 1.3, 1.4, 1.4.1, 1.4.4, 1.4.5, 1.4.6, 1.4.8, 1.4.9, 2.0.5, 2.1.0) ERROR: No matching distribution found for mob-suite==3.0.3

cedric

From: Kirill Bessonov @.***> Sent: May 3, 2022 13:20 To: phac-nml/mob-suite Cc: Computational Methods for Comparative Genomics at Simon Fraser University; Author Subject: Re: [phac-nml/mob-suite] Circlator (Issue #106)

I would just run pip3 install --ignore-installed --force-reinstall mob-suite==3.0.3. This way if there are any residual temporary packages, the install will overwrite them mimicking a fresh install. If installing via pip3 you would need to manually install dependencies (mash and blast+). If running Ubuntu they can be installed via apt install mash ncbi-blast+ -y. Here is a docker file that lists all install commands from scratch on clean Linux system https://github.com/phac-nml/mob-suite/blob/master/mob_suite/docker/Dockerfile.

— Reply to this email directly, view it on GitHubhttps://github.com/phac-nml/mob-suite/issues/106#issuecomment-1116525705, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACXV7DTAXFMEL7B3N4BQJFTVIGAVZANCNFSM5UUCYKWQ. You are receiving this because you authored the thread.Message ID: @.***>

kbessonov1984 commented 2 years ago

Salut Cedric, Which version of python are you running on the CC cluster? Looks like pip3 does not see any mob-suite versions 3.0.0 and greater. The full list of versions could be found at https://pypi.org/project/mob-suite/#history. You can try to provide full path to the remote install file like so pip3 install --ignore-installed --force-reinstall https://files.pythonhosted.org/packages/4c/08/c509a168fcadb04f5124a50827ec58a8c598b2c24032fc38cf488e0488c1/mob_suite-3.0.3.tar.gz. Perhaps pip3 only uses local package wheels and does not connect to remote PyPI repo?

I tried to install the version 3.0.3 on Ubuntu 20.04 and python version 3.8 and no issues as seen below. I guess you are using Python virtual environment? Try to re-create a new virtual environment with the newest python version available on the cluster.

root@518f2c37f434:/# pip3 install --ignore-installed --force-reinstall mob-suite==3.0.3
Collecting mob-suite==3.0.3
  Using cached mob_suite-3.0.3.tar.gz (203 kB)
Collecting biopython<2,>=1.70
  Using cached biopython-1.79-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB)
Collecting ete3<4,>=3.0
  Using cached ete3-3.1.2.tar.gz (4.7 MB)
Collecting numpy<2,>=1.11.1
  Using cached numpy-1.23.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Collecting pandas<=1.0.5,>=0.22.0
  Using cached pandas-1.0.5-cp38-cp38-manylinux1_x86_64.whl (10.0 MB)
Collecting pycurl<8,>=7.43.0
  Using cached pycurl-7.45.1.tar.gz (233 kB)
Collecting pyqt5<6,>=5.0
  Downloading PyQt5-5.15.7-cp37-abi3-manylinux1_x86_64.whl (8.4 MB)
     |████████████████████████████████| 8.4 MB 3.2 MB/s
Collecting scipy<2,>=1.1.0
  Downloading scipy-1.9.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.8 MB)
     |████████████████████████████████| 33.8 MB 7.9 MB/s
Collecting six<2,>=1.10
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting tables<4,>=3.3.0
  Downloading tables-3.7.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.9 MB)
     |████████████████████████████████| 5.9 MB 812 kB/s
Collecting pytz>=2017.2
  Downloading pytz-2022.4-py2.py3-none-any.whl (500 kB)
     |████████████████████████████████| 500 kB 3.2 MB/s
Collecting python-dateutil>=2.6.1
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     |████████████████████████████████| 247 kB 5.0 MB/s
Collecting PyQt5-sip<13,>=12.11
  Downloading PyQt5_sip-12.11.0-cp38-cp38-manylinux1_x86_64.whl (361 kB)
     |████████████████████████████████| 361 kB 7.0 MB/s
Collecting PyQt5-Qt5>=5.15.0
  Downloading PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (59.9 MB)
     |████████████████████████████████| 59.9 MB 121 kB/s
Collecting numexpr>=2.6.2
  Downloading numexpr-2.8.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (381 kB)
     |████████████████████████████████| 381 kB 6.4 MB/s
Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     |████████████████████████████████| 40 kB 3.8 MB/s
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     |████████████████████████████████| 98 kB 4.4 MB/s
Building wheels for collected packages: mob-suite, ete3, pycurl
  Building wheel for mob-suite (setup.py) ... done
  Created wheel for mob-suite: filename=mob_suite-3.0.3-py3-none-any.whl size=207446 sha256=cb466f29fe339b26a3858f5fd7f83da64e2e2df92532fcad89624d349240ef59
  Stored in directory: /root/.cache/pip/wheels/a3/00/1a/5a35264b607fa2377485fe9a8e2b9366d8594292218960f460
  Building wheel for ete3 (setup.py) ... done
  Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2272998 sha256=02b94e812794a53beb85bc8cc2703e4b90e0376b96200110620019f7a23859b7
  Stored in directory: /root/.cache/pip/wheels/78/96/a0/973292c4813e6b39b611bec535521655088425516959768f46
  Building wheel for pycurl (setup.py) ... done
  Created wheel for pycurl: filename=pycurl-7.45.1-cp38-cp38-linux_x86_64.whl size=339593 sha256=6c23c2ea68b5ca6fbca564abce7939fb853ebcc7faba59ba6892494f67686413
  Stored in directory: /root/.cache/pip/wheels/29/9b/97/525e19354d667ab6a101620502bd1df957057f66bee218305d
Successfully built mob-suite ete3 pycurl
Installing collected packages: numpy, biopython, ete3, pytz, six, python-dateutil, pandas, pycurl, PyQt5-sip, PyQt5-Qt5, pyqt5, scipy, pyparsing, packaging, numexpr, tables, mob-suite
Successfully installed PyQt5-Qt5-5.15.2 PyQt5-sip-12.11.0 biopython-1.79 ete3-3.1.2 mob-suite-3.0.3 numexpr-2.8.3 numpy-1.23.3 packaging-21.3 pandas-1.0.5 pycurl-7.45.1 pyparsing-3.0.9 pyqt5-5.15.7 python-dateutil-2.8.2 pytz-2022.4 scipy-1.9.2 six-1.16.0 tables-3.7.0