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nedialkova-lab / mim-tRNAseq

Modification-induced misincorporation tRNA sequencing
GNU General Public License v3.0
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GMAP version 2017-11-15 #67

Closed Futa0908 closed 1 month ago

Futa0908 commented 11 months ago

Hi, there. When installing mimseq using conda-forge according to the protocol, the version of GSNAP-GMAP becomes 2017-11-15 instead of 2019-02-26 and mimseq does not work properly. What should I do in such a case? Is it?

nedialkova-lab commented 11 months ago

I suggest deleting the environment and repeating the installation process - the GSNAP version that came with mimseq1.3.8 installed with mamba was 2019-02-26 for me.

drewjbeh commented 11 months ago

Hi there,

One issue with conda is that it is known to have problems with reproducibility (see this for example). That is, the environments can look different on different machines. The issue might be your conda version. I am using conda 23.3.1 installed with the miniforge installer. Unfortunately, for whatever reason, your environment ends up with the wrong GMAP version. If repeating the environment installation as suggested, or perhaps installing conda with the same version as me does not help, I would suggest manually upgrading GMAP/GSNAP using mamba in your environment. This should be painless and quick, and will hopeful work. Unfortunately, due to conda's complicated depenency handling, I cannot change anything in the conda package without breaking things. Hope this helps.

vcognat commented 9 months ago

Hi, I had the same issue and upgrading didn't work. To solve the problem I installed GSNAP 2019-02-26 in my conda env before installing mimseq. Hope this can help someone ...

nedialkova-lab commented 9 months ago

Great thanks for that!