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GenomicsAotearoa / long-read-assembly

Long-read assembly workshop
https://genomicsaotearoa.github.io/long-read-assembly/
GNU General Public License v3.0
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verkko module is missing pandas extension #1

Closed DininduSenanayake closed 1 year ago

DininduSenanayake commented 1 year ago
verkko_module_pandaserror
DininduSenanayake commented 1 year ago

Fixed now 

$ module load verkko/1.3.1-Miniconda3 

$ pip freeze | grep pandas
pandas==1.5.3
abueg commented 1 year ago

hi @DininduSenanayake ! quick question about the verkko install, did you install the conda version or build from source? just checking as I think the conda version installed might be behind:

08:05:52 mahuika01 ~ $ module load verkko
08:08:55 mahuika01 ~ $ verkko --version
bioconda verkko bioconda 1.0

vs a version on my uni's HPC:

[labueg@login04 /lustre/fs5/vgl/store/labueg/programs]$ conda activate verkko_1.3.1
(verkko_1.3.1) [labueg@login04 /lustre/fs5/vgl/store/labueg/programs]$ which verkko
/vggpfs/fs3/vgl/store/labueg/anaconda3/envs/verkko_1.3.1/bin/verkko
(verkko_1.3.1) [labueg@login04 /lustre/fs5/vgl/store/labueg/programs]$ verkko --version
bioconda verkko bioconda 1.3.1
DininduSenanayake commented 1 year ago

@abueg Ah...I did the conda install. Will try to fix ASAP and get the version 1.3.1 up and running

DininduSenanayake commented 1 year ago

@abueg This is fixed now

$ module load verkko/1.3.1-Miniconda3

$ verkko --version
bioconda verkko bioconda 1.3.1