wook2014

An error with blast.py and base.py

2

I have tried to run ``` python -m jcvi.compara.catalog ortholog G1 G9 --no_strip_names --cpu=35 ``` but an error occured ``` Traceback (most recent call last): File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/runpy.py", line 197, in...

How to use smart annotation mode in local eggnog-mapper

2

I have noticed that eggnog-mapper server online (http://eggnog-mapper.embl.de/) can use smart annotation to form a output file. How could I use smart annotation when I run eggnog-mapper on my local...

libgsl.so.25: cannot open shared object file

2

I have installed mashmap through conda, with version mashmap-2.0-pl5321h8e5b204_8, but it shows error " libgsl.so.25: cannot open shared object file". I checked on anaconda that the requirement of this version...

treeio read tree files form nexus format with extra quotation marks

3

Dear @GuangchuangYu I recently use ggtree to process my phylogenetic tree. I obtained the tree file through IQTree and exported the file in nexus format by figtree. But I meet...

**Describe of the bug** I tried to install macs3 in conda with the following command. ``` conda install -c maximinio macs3 ``` For the first time when installed without specific...

MACS2 steps did not carried out

2

### Description of the bug I have run chipseq workflow and I can not find the MACS2 result. I have checked the log file and it seemed that the steps...

Error with sklearn on installing by pip

6

I am trying to install altanalyze in a conda environment on linux server. I tried to install directly by `pip install AltAnalyze` but there comes an error: ``` ERROR: Command...

I installed ssbio with python 3.10 and ipywidgets 7.0.0, an error occured: ``` Traceback (most recent call last): File "", line 1, in File "/home/wook/.local/lib/python3.10/site-packages/nglview/__init__.py", line 4, in from ....

Error on "count column is missing in your data"

2

Appreciate for creating such a good package. I meet up with a problem when using ggpie with summarized data. I have my data like this: ``` dt

I have recently deal with a perturb-seq data from 10X CRISPR-Screening and output from cellranger. the features file have 3 columns: ensemble, gene_name, feature_type. When I read in the by...