saketkc

library(dplyr)
library(httr)
library(rvest)
library(xml2)
library(stringr)
library(DT)
library(htmltools)


domains_to_remove <- c(

saketkc

library(biomaRt)
species_tx2gene_map = c(
    "btaurus",
    "mauratus",
    "mmulatta",
    "ggallus",
    "sscrofa",
    "mmusculus",
    "dreiro")
    "rnorvegicus",

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@HD	VN:1.6	SO:coordinate
@SQ	SN:chr1	LN:248956422
@SQ	SN:chr10	LN:133797422
@SQ	SN:chr11	LN:135086622
@SQ	SN:chr12	LN:133275309
@SQ	SN:chr13	LN:114364328
@SQ	SN:chr14	LN:107043718
@SQ	SN:chr15	LN:101991189
@SQ	SN:chr16	LN:90338345
@SQ	SN:chr17	LN:83257441

saketkc

NVML: Driver/library version mismatch

Need to unload the the Nvidia driver kernel module (kmod) and then load it again as the current version is wrong.

Which drivers are loaded?

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#!/usr/bin/env python
# coding: utf-8

# In[1]:


from collections import defaultdict, OrderedDict
import warnings
import gffutils
import pybedtools

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import re
import sys
import os

sys.path = ['', '/env/python', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/site-packages', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages', '/usr/local/lib/python3.6/dist-packages/IPython/extensions', '/root/.ipython']

print('***********************************************************************')
print('Let us check on those pyarrow and cffi versions...')
print('***********************************************************************')
print()

saketkc

#!/bin/bash
set -eox pipefail
#python -c "import sys, os; dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages'); sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]; sys.path.append('/usr/local/lib/python3.6/site-packages/'); exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
python -c "import sys, os; ['', '/env/python', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/site-packages', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages', '/usr/local/lib/python3.6/site-packages/']; exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
nvcc --version
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai

saketkc

#!/bin/bash
set -eox pipefail
python -c "import sys, os; dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages'); sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]; sys.path.append('/usr/local/lib/python3.6/site-packages/'); exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
nvcc --version
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai
conda install -y dask-cuda dask-cudf cuml cugraph numba=0.48* scipy ucx-py ucx-proc=*=gpu scikit-learn louvain cupy=7 scanpy umap-learn pip

saketkc

#!/bin/bash
set -eox pipefail
#echo "#!/usr/bin/env python
#import sys, os
#print(sys.path)
#dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages')
#print(dist_package_index)
#sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]
#sys.path.append('/usr/local/lib/python3.6/site-packages/')
#print(sys.path)

saketkc

#!/bin/bash
set -eox pipefail
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai
pip install git+https://github.com/dask/dask.git
pip install git+https://github.com/dask/distributed.git
conda install -y cuml cugraph louvain scanpy cudf cupy umap-learn scikit-learn numba>=0.48* leidenalg r-seurat r-reticulate