Conda installation Majiq not working anymore

[santataRU]

Dear All,

I attempted to install Majiq via Conda following the instructions on this webpage: https://majiq.biociphers.org/norton_et_al_2017/. However, the installation was unsuccessful, and it seems that the instructions may be outdated.

Could you suggest any updated methods or easier ways to install this package?

Thank you very much for your help.

Best regards,
Xiao

[aleighbrown]

HI there,
Sorry for the delayed response.
I'd recommend going through the academic download page and get the instructions after you sign the waiver that its for academic purposes (if it is) and create a conda env called 'majiq'

https://majiq.biociphers.org/app_download/

You could also give Baltica a try and use the MAJIQ singularity/dock container they provide - I'm not sure which version that is though tbh

https://github.com/dieterich-lab/Baltica

[santataRU]

Hi, Anna, Thank you. I tried to install Majiq 2.2 with the Baltica Dockerfile (attached), but I failed with the error attached at the end. Regards, Xiao (snakemake) ***@***.*** majiq_academic % docker build -t majiq_image . [+] Building 5.1s (11/14) docker:desktop-linux => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 1.08kB 0.0s => [internal] load metadata for docker.io/library/ubuntu:20.04 0.2s => [internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [ 1/11] FROM ***@***.***:8e5c4f0285ecbb4ead070431d29b576a530d3166df73ec44affc1cd27555141b 0.0s => => resolve ***@***.***:8e5c4f0285ecbb4ead070431d29b576a530d3166df73ec44affc1cd27555141b 0.0s => CACHED [ 2/11] RUN apt-get -y update 0.0s => CACHED [ 3/11] RUN apt-get -y install libhts-dev python3-dev python3-pip git gcc 0.0s => CACHED [ 4/11] WORKDIR /tmp 0.0s => CACHED [ 5/11] RUN git clone https://bitbucket.org/biociphers/majiq_academic.git 0.0s => CACHED [ 6/11] WORKDIR majiq_academic 0.0s => CACHED [ 7/11] RUN pip3 install --no-cache-dir -U pip 0.0s => ERROR [ 8/11] RUN pip3 install --no-cache-dir ./voila 4.9s

------ [ 8/11] RUN pip3 install --no-cache-dir ./voila: 0.233 Processing ./voila 0.235 Installing build dependencies: started 1.110 Installing build dependencies: finished with status 'done' 1.110 Getting requirements to build wheel: started 1.439 Getting requirements to build wheel: finished with status 'done' 1.440 Preparing metadata (pyproject.toml): started 1.684 Preparing metadata (pyproject.toml): finished with status 'done' 1.712 Collecting Click==7.1.2 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.726 Downloading click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB) 1.834 Collecting cryptography==41.0.5 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.838 Downloading cryptography-41.0.5-cp37-abi3-manylinux_2_28_aarch64.whl.metadata (5.2 kB) 1.853 Collecting Flask==1.1.4 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.859 Downloading Flask-1.1.4-py2.py3-none-any.whl.metadata (4.6 kB) 1.866 Collecting Flask-Session==0.3.1 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.872 Downloading Flask_Session-0.3.1-py2.py3-none-any.whl.metadata (900 bytes) 1.880 Collecting Flask-WTF==0.14.2 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.884 Downloading Flask_WTF-0.14.2-py2.py3-none-any.whl.metadata (1.8 kB) 1.890 Collecting gitdb2==2.0.6 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.894 Downloading gitdb2-2.0.6-py2.py3-none-any.whl.metadata (1.1 kB) 1.910 Collecting GitPython==3.0.5 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.914 Downloading GitPython-3.0.5-py3-none-any.whl.metadata (1.1 kB) 1.921 Collecting gtfparse==2.0.1 (from rna_voila==2.5.8.dev1+g9eebd1fc) 1.925 Downloading gtfparse-2.0.1.tar.gz (17 kB) 1.929 Preparing metadata (setup.py): started 2.010 Preparing metadata (setup.py): finished with status 'done' 2.028 Collecting gunicorn==19.9.0 (from rna_voila==2.5.8.dev1+g9eebd1fc) 2.032 Downloading gunicorn-19.9.0-py2.py3-none-any.whl.metadata (3.4 kB) 2.064 Collecting h5py==3.11.0 (from rna_voila==2.5.8.dev1+g9eebd1fc) 2.068 Downloading h5py-3.11.0.tar.gz (406 kB) 2.109 Installing build dependencies: started 4.307 Installing build dependencies: finished with status 'done' 4.308 Getting requirements to build wheel: started 4.445 Getting requirements to build wheel: finished with status 'done' 4.446 Preparing metadata (pyproject.toml): started 4.582 Preparing metadata (pyproject.toml): finished with status 'done' 4.589 Collecting intervaltree==3.1.0 (from rna_voila==2.5.8.dev1+g9eebd1fc) 4.593 Downloading intervaltree-3.1.0.tar.gz (32 kB) 4.598 Preparing metadata (setup.py): started 4.688 Preparing metadata (setup.py): finished with status 'done' 4.701 Collecting itsdangerous==1.1.0 (from rna_voila==2.5.8.dev1+g9eebd1fc) 4.706 Downloading itsdangerous-1.1.0-py2.py3-none-any.whl.metadata (3.1 kB) 4.715 Collecting Jinja2==2.11.1 (from rna_voila==2.5.8.dev1+g9eebd1fc) 4.720 Downloading Jinja2-2.11.1-py2.py3-none-any.whl.metadata (3.5 kB) 4.752 Collecting MarkupSafe==1.1.1 (from rna_voila==2.5.8.dev1+g9eebd1fc) 4.757 Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux2014_aarch64.whl.metadata (3.2 kB) 4.772 INFO: pip is looking at multiple versions of rna-voila to determine which version is compatible with other requirements. This could take a while. 4.774 ERROR: Ignored the following yanked versions: 2.6, 2.6.1 4.774 ERROR: Ignored the following versions that require a different python version: 1.2.2 Requires-Python >=3.9; 3.0.0 Requires-Python >=3.9; 3.0.1 Requires-Python >=3.9; 3.0.2 Requires-Python >=3.9; 3.1.0 Requires-Python

=3.9; 3.12.0 Requires-Python >=3.9; 3.12.1 Requires-Python >=3.9; 3.2

Requires-Python >=3.9; 3.2.1 Requires-Python >=3.9; 3.2rc0 Requires-Python

=3.9; 3.3 Requires-Python >=3.10; 3.3rc0 Requires-Python >=3.10; 3.4

Requires-Python >=3.10; 3.4.1 Requires-Python >=3.10; 3.4.2 Requires-Python

=3.10; 3.4rc0 Requires-Python >=3.10

4.774 ERROR: Could not find a version that satisfies the requirement networkx==3.3 (from rna-voila) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4, 2.5rc1, 2.5, 2.5.1, 2.6rc1, 2.6rc2, 2.6.2, 2.6.3, 2.7rc1, 2.7, 2.7.1, 2.8rc1, 2.8, 2.8.1rc1, 2.8.1, 2.8.2, 2.8.3, 2.8.4, 2.8.5, 2.8.6, 2.8.7, 2.8.8, 3.0b1, 3.0rc1, 3.0, 3.1rc0, 3.1) 4.811 ERROR: No matching distribution found for networkx==3.3

…

------ Dockerfile:15

-------------------- 13 | WORKDIR majiq_academic 14 | RUN pip3 install --no-cache-dir -U pip 15 | >>> RUN pip3 install --no-cache-dir ./voila 16 | RUN pip3 install --no-cache-dir ./majiq 17 | WORKDIR /tmp

-------------------- ERROR: failed to solve: process "/bin/sh -c pip3 install --no-cache-dir ./voila" did not complete successfully: exit code: 1

On Wed, Nov 13, 2024 at 9:34 AM Anna-Leigh Brown ***@***.***> wrote: HI there, Sorry for the delayed response. I'd recommend going through the academic download page and get the instructions after you sign the waiver that its for academic purposes (if it is) and create a conda env called 'majiq' https://majiq.biociphers.org/app_download/ You could also give Baltica a try and use the MAJIQ singularity/dock container they provide - I'm not sure which version that is though tbh https://github.com/dieterich-lab/Baltica — Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMMRAYPDSJ7CEYAFSCKEI232ANPRBAVCNFSM6AAAAABRQSVFHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTG44TMNRYGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>