aws ec2 miniforge3 conda

 

source ~/miniforge3/etc/profile.d/conda.sh

conda init bash

source ~/.bashrc

conda create -n dpgr310 python=3.10 -y

conda activate dpgr310

(dpgr310) pip install -r requirements.txt

# or at least:

(dpgr310) pip install pandas

ts conda tsR403, tidyverse, EpiNow2 installation

# THIS DID NOT WORK

-bash-4.2$ module load anaconda/5.2.0 

-bash-4.2$ conda create --name tsR403

Collecting package metadata: done

Solving environment: done

## Package Plan ##

  environment location: /home/hqin/.conda/envs/tsR403

Proceed ([y]/n)? y  

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

#

# To activate this environment, use

#

#     $ conda activate tsR403

#

# To deactivate an active environment, use

#

#     $ conda deactivate

-bash-4.2$ 

 -bash-4.2$ conda activate tsR403

(tsR403) -bash-4.2$ conda install -c conda-forge libv8

Collecting package metadata: done

Hong then run R

install.packages('tidyverse') #this seem to worked. 

-----------------------------[ ANTICONF ]-------------------------------

Configuration failed to find the libv8 engine library. Try installing:

 * deb: libv8-dev or libnode-dev (Debian / Ubuntu)

 * rpm: v8-devel (Fedora, EPEL)

 * brew: v8 (OSX)

 * csw: libv8_dev (Solaris)

To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:

R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

---------------------------[ ERROR MESSAGE ]----------------------------

<stdin>:1:16: fatal error: v8.h: No such file or directory

compilation terminated.

-------------------------------------------------------

(tsR403) -bash-4.2$ conda install -c conda-forge r-randomcolor

Collecting package metadata: \ 

#this install many packages

Ref: https://github.com/iaconogi/bigSCale2/issues/19

I then tried:

R: install.packages('EpiNow2') #this seems to be running now. 

library(EpiNow2) #it worked!

install.packages('woldmet')

#The entire install seem to take almost 2 hours. 

Checked a few hour later, EpiNow2 installation did not work. 

gffutils, big macbook pro

Ref https://daler.github.io/gffutils/installation.html

(base) CS313BQin:aln2snps hqin$ conda  create -n gff python=3.7 anaconda

Accept 'y', many things are added. 

(base) CS313BQin:aln2snps hqin$ conda activate gff

(gff) CS313BQin:aln2snps hqin$ 

(gff) CS313BQin:aln2snps hqin$ conda install --channel bioconda pybedtools bedtools biopython

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /opt/anaconda3/envs/gff

  added / updated specs:

    - bedtools

    - biopython

    - pybedtools

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    bedtools-2.29.2            |       h37cfd92_0         868 KB  bioconda

    biopython-1.77             |   py37haf1e3a3_0         2.1 MB

    libdeflate-1.0             |       h1de35cc_1          45 KB  bioconda

    pybedtools-0.8.1           |   py37h2dec4b4_0        12.1 MB  bioconda

    pysam-0.15.3               |   py37h726f235_1         2.1 MB  bioconda

    ------------------------------------------------------------

                                           Total:        17.1 MB

The following NEW packages will be INSTALLED:

  bedtools           bioconda/osx-64::bedtools-2.29.2-h37cfd92_0

  biopython          pkgs/main/osx-64::biopython-1.77-py37haf1e3a3_0

  libdeflate         bioconda/osx-64::libdeflate-1.0-h1de35cc_1

  pybedtools         bioconda/osx-64::pybedtools-0.8.1-py37h2dec4b4_0

  pysam              bioconda/osx-64::pysam-0.15.3-py37h726f235_1

(gff) CS313BQin:aln2snps hqin$ conda install --channel bioconda gffutils

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /opt/anaconda3/envs/gff

  added / updated specs:

    - gffutils

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    argcomplete-1.11.1         |             py_1          36 KB

    gffutils-0.10.1            |             py_0         1.2 MB  bioconda

    pyfaidx-0.5.9              |     pyh4c3bd37_0          28 KB  bioconda

    simplejson-3.17.0          |   py37h1de35cc_0          98 KB

    ------------------------------------------------------------

                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

  argcomplete        pkgs/main/noarch::argcomplete-1.11.1-py_1

  gffutils           bioconda/noarch::gffutils-0.10.1-py_0

  pyfaidx            bioconda/noarch::pyfaidx-0.5.9-pyh4c3bd37_0

  simplejson         pkgs/main/osx-64::simplejson-3.17.0-py37h1de35cc_0

Proceed ([y]/n)? 

see https://daler.github.io/gffutils/examples.html

In shell python, it worked using in-memory database. 

(gff) CS313BQin:aln2snps hqin$ python

Python 3.7.7 (default, Mar 26 2020, 10:32:53) 

[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import gffutils

>>> fn = gffutils.example_filename('mouse_extra_comma.gff3')

>>> db = gffutils.create_db(fn, ':memory:')

>>> db

<gffutils.interface.FeatureDB object at 0x7f9568158b90>

>>> 

Package path 

>> import sys

>>> sys.path

['', '/opt/anaconda3/envs/gff/lib/python37.zip', '/opt/anaconda3/envs/gff/lib/python3.7', '/opt/anaconda3/envs/gff/lib/python3.7/lib-dynload', '/opt/anaconda3/envs/gff/lib/python3.7/site-packages', '/opt/anaconda3/envs/gff/lib/python3.7/site-packages/aeosa']

>>>