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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error in installation #822

Closed jmpe77 closed 3 months ago

jmpe77 commented 3 months ago

I am trying to install SqueezeMeta in Ubuntu 22.04.4. Installation using mamba did not work so I tried downloading the latest release from the repository. After following all the instructions for the installation, I run the test_install.pl and it showed the following errors

WARNING: Some SqueezeMeta dependencies could not be found in your environment or failed to execute!

jmpe77 commented 3 months ago

Checking binaries spades.py NOT OK ERROR: Error running cd /tmp/tmp.MeXsEdvJY1; spades.py --test metabat2 NOT OK ERROR: Error running metabat2 -h jgi_summarize_bam_contig_depths NOT OK ERROR: Error running jgi_summarize_bam_contig_depths -h samtools NOT OK ERROR: Error running samtools --version bwa OK minimap2 OK diamond OK hmmsearch OK cd-hit-est OK kmer-db NOT OK ERROR: Error running kmer-db -h aragorn OK mothur NOT OK ERROR: Error running mothur -h

fpusan commented 3 months ago

If possible, create a conda environment with spades, metabat2, samtools, kmer-db and mothur, and try to run test_install.pl from there.

We used to redistribute those binaries (we still do, technically) but they were creating compatibility issues with newer versions of Ubuntu and other distros so we switched to conda in order to have a "one size fits all" solution.

If conda is not possible for you, you will need to install those manually (possible compiling from source) and make then available in your path.

jmpe77 commented 3 months ago

I see, then maybe it is better to figure out what happened with my installation with conda.

This is what I got when trying to install it with conda

Looking for: ['squeezemeta']

anaconda/linux-64 No change bioconda/linux-64 No change conda-forge/linux-64 No change bioconda/noarch No change conda-forge/noarch No change pkgs/r/linux-64 No change pkgs/main/noarch No change anaconda/noarch No change pkgs/main/linux-64 No change fpusan/linux-64 No change fpusan/noarch No change pkgs/r/noarch No change warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY Could not solve for environment specs The following packages are incompatible └─ squeezemeta is not installable because there are no viable options ├─ squeezemeta [1.1.0|1.1.1|...|1.6.2post1] would require │ └─ ruby 2.5.* but there are no viable options │ ├─ ruby [2.5.1|2.5.5|2.5.7] conflicts with any installable versions previously reported; │ └─ ruby 2.5.1 would require │ └─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel); └─ squeezemeta [1.6.2post2|1.6.2post3|1.6.3] would require └─ biopython 1.81 , which conflicts with any installable versions previously reported.

fpusan commented 3 months ago

What's your OS/distros/version? What exact command are you using? Do you have a ~/.condarc file in place?

jmpe77 commented 3 months ago

I have Ubuntu 2.04

I am using this command mamba create -n SqueezeMeta -c bioconda -c conda-forge -c anaconda -c fpusan squeezemeta -no-channel-priority

i don't think I have a .condarc file

fpusan commented 3 months ago

Try with mamba create -n SqueezeMeta -c conda-forge -c bioconda -c anaconda -c fpusan squeezemeta=1.6 --no-channel-priority

jmpe77 commented 3 months ago

Thank you very much. Now the test_install sows everything OK.

fpusan commented 3 months ago

Glad to hear. Closing issue