Bioconda installation

[ChemaMD]

Hi,

Thanks for the great package. I'm trying to install GimmeMotifs via conda and it keeps failing (in different computers and users). The command I run, as per guides in readthedocs:

conda create -n gimme gimmemotifs

Output:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: /

In case it is useful, below the info of my conda installation.

Thanks for your help!

Chema

====== conda info =====

conda version : 4.13.0
conda-build version : 3.21.9
python version : 3.8.13.final.0
virtual packages : __osx=10.16=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/anaconda3 (writable)
conda av data dir : /opt/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/osx-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
platform : osx-64
user-agent : conda/4.13.0 requests/2.28.0 CPython/3.8.13 Darwin/21.4.0 OSX/10.16
UID:GID : 502:20
netrc file : None
offline mode : False

[paolabc]

Yes, I had the same problem. Maybe, a solution is to install it via source code. Download it from here https://anaconda.org/bioconda/gimmemotifs/files and install it by using the command conda install --offline name_of_the_file_package. There are other alternatives to install this tool and it is described in the instalation section here https://gimmemotifs.readthedocs.io/en/stable/installation.html. :)

[paolabc]

I also would like to know why this problem of conda installation for this tool is happened. Conda install is an easy and friendly way.

[siebrenf]

Hey @ChemaMD and @paolabc,
GimmeMotifs if using a big bunch of big packages for motif discovery. It seems Conda is really unhappy with one or both of those two. I'm trying to fix the root cause (by splitting the gimmemotifs conda recipe), but this is still a work in progress...

Aside from @paolabc's excellent suggestions, here are two additional methods to fix Conda (for all big packages, not just gimmemotifs):

• Conda itself is working on these kinds of issues, and has an experimental fix that you can find here.
• You can use conda to install mamba, and then use mamba as if you're using conda (but faster!):

  conda install -c conda-forge conda=4.13 mamba=0.24
  mamba create -n gimme gimmemotifs
  

[paolabc]

Hi
Thank you for your quicly reply. I got it. And I just tried it here and it works as well. :)

[ChemaMD]

Hi, thanks for the suggestions, I'll def give it a go!

[Pooran-Dewari]

Thanks @siebrenf , mamba works like a charm. I had given up with conda but just came across your advice, lifesaving.

[shaunmahony]

I found the same problem with conda. The pip install method works, however.

[IanCodes]

Has there been any movement on this issue?
I tried installing via mamba, but get an out of memory error.
I also tried the local install method by downloading files from Anaconda:
https://anaconda.org/bioconda/gimmemotifs/0.17.1/download/linux-64/gimmemotifs-0.17.1-py38h8ded8fe_1.tar.bz2

conda install --offline gimmemotifs-0.17.1-py38h8ded8fe_1.tar.bz2

This appeared to work:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

However, trying to run gimme results in:
(gimme) $ gimme
Traceback (most recent call last):
File "/mnt/fls01-home01/mqbssid3/.conda/envs/gimme/bin/gimme", line 8, in <module>
from gimmemotifs.cli import cli
ModuleNotFoundError: No module named 'gimmemotifs'

I would like to revisit this tool, but conda isn't helping.

Thanks.

[siebrenf]

This is ongoing, here is a little overview and two potential fixes:

Overview:

• I am trying to get a better gimmemotifs version on bioconda (with all motif discovery tools & for more python versions). This is stuck due to memory limitations.
  • The people over at bioconda are working on a potential fix for the memory limitations.
• The people over at conda are working on improving conda's solver (replacing theirs with mamba's).

Fixes:

• The Gimmemotifs bioconda package is split in two! If you do not need motif discovery tools (for instance, when you are using one of the built in motif databases), try gimmemotifs-minimal.
• You can reduce the memory requirements of the installation of any conda package by installing it in a new conda environment:

# install mamba if you haven't already
conda install -c conda-forge mamba

# create a new environment with gimmemotifs
NAME=gimme
mamba create -n $NAME gimmemotifs

# give it a try
conda activate $NAME
gimme --help

[IanCodes]

Thank you @siebrenf. I tried the mamba method again on a different system. It installed, but I get the following error:
ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Any thoughts?

I am using Ubuntu 20 if that helps.

Thank you.

[siebrenf]

Some of our dependencies are outdated on bioconda, and throw this error occasionally (it is likely one of the ucsc tools). This behavior is not consistent, so you might be OK if you run it again...

[IanCodes]

I thought I made progress, but get the following:
`
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.31=0
• feature:|@/linux-64::__glibc==2.31=0
• gimmemotifs -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31
`

I am not sure how to interpret this, but don't I have a never version of glibc than requested?

Thank you.

[siebrenf]

That's a conda error right? It seems you are trying to install something new in the environment that is clashing with something already in there... Easiest solution is to simply create a new environment :)

Btw, i am trying to release a new version of gimmemotifs on bioconda that is easier to install (0.17.2). Hopefully done on monday!

[IanCodes]

@siebrenf thanks for the reply. It was a new environment:
conda create -n gimme python=3

I'll try the new release next week.

[IanCodes]

Unfortunately, the new version doesn't install either.
conda create -n gimme python=3
conda install gimmemotifs

Resulted in "Solving environment:" running for three days before I stopped it.

[siebrenf]

Hey Ian,

This command should work within minutes: mamba create -n gimme gimmemotifs=0.17.2.
You can specify which python version you want with it (3.7-3.10, default is 3.10. I tested with 3.8): mamba create -n gimme gimmemotifs=0.17.2 python=3.8.

[IanCodes]

@siebrenf just to say I successfully installed gimmemotifs via mamba. Thank you for your help.

[foryoubar]

Hello，I’ve tried to install gimmemotifs according to the instructions on the official website, I ran the following command：
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda install -c conda-forge "conda>=4.12" "mamba>=0.27"
After mamba installed, I ran "mamba install gimmemotif", but got a " Could not solve for environment specs
The following package could not be installed
└─ gimmemotif does not exist (perhaps a typo or a missing channel)"
Could you please help me deal with this bug? Thank you!

[simonvh]

Can you try: mamba install gimmemotifs (With an s at the end)

[foryoubar]

Sure. I tried this command ”mamba install gimmemotifs“before, and it showed the same error.

[siebrenf]

Your current conda environment might be incompatible. You can create a fresh environment with

mamba create -n gimme gimmemotifs

[foryoubar]

Thank you sincerely for your patient reply! I will follow your suggestion and try to install it again later.

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