学习小组Day3笔记-wang
2022-04-20 本文已影响0人
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bio16@VM-0-6-ubuntu:~$ uname -a
Linux VM-0-6-ubuntu 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
bio16@VM-0-6-ubuntu:~$ ls -l
total 32
drwxrwxr-x 2 bio16 bio16 4096 Apr 19 20:41 biosoft
-rw-rw-r-- 1 bio16 bio16 32 Apr 19 20:56 haha.txt
-rw-rw-r-- 1 bio16 bio16 63 Apr 19 21:10 hello_world.txt
-rw-rw-r-- 1 bio16 bio16 63 Apr 19 21:29 home2.txt
-rw-rw-r-- 1 bio16 bio16 63 Apr 19 21:20 home.txt
drwxrwxr-x 2 bio16 bio16 4096 Apr 19 20:41 project
drwxrwxr-x 2 bio16 bio16 4096 Apr 19 20:41 src
drwxrwxr-x 2 bio16 bio16 4096 Apr 19 21:31 tmp
bio16@VM-0-6-ubuntu:~$ cd biosoft
bio16@VM-0-6-ubuntu:~/biosoft$ pwd
/home/bio16/biosoft
bio16@VM-0-6-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
--2022-04-20 19:12:47-- https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
Resolving mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)... 101.6.15.130, 2402:f000:1:400::2
Connecting to mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)|101.6.15.130|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 75660608 (72M) [application/octet-stream]
Saving to: ‘Miniconda3-py39_4.11.0-Linux-x86_64.sh’
Miniconda3-py39_4.1 100%[===================>] 72.16M 2.69MB/s in 21s
2022-04-20 19:13:09 (3.41 MB/s) - ‘Miniconda3-py39_4.11.0-Linux-x86_64.sh’ saved [75660608/75660608]
bio16@VM-0-6-ubuntu:~/biosoft$ ls -l -h
total 73M
-rw-rw-r-- 1 bio16 bio16 73M Feb 16 03:08 Miniconda3-py39_4.11.0-Linux-x86_64.sh
bio16@VM-0-6-ubuntu:~/biosoft$ conda
conda: command not found
bio16@VM-0-6-ubuntu:~/biosoft$ bash Miniconda3-py39_4.11.0-Linux-x86_64.sh
Welcome to Miniconda3 py39_4.11.0
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
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Last updated June 24, 2021
Do you accept the license terms? [yes|no]
[no] >>>
Please answer 'yes' or 'no':'
>>> yes
Miniconda3 will now be installed into this location:
/home/bio16/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/bio16/miniconda3] >>>
PREFIX=/home/bio16/miniconda3
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio16/miniconda3
added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==4.5=1_gnu
- brotlipy==0.7.0=py39h27cfd23_1003
- ca-certificates==2021.10.26=h06a4308_2
- certifi==2021.10.8=py39h06a4308_2
- cffi==1.15.0=py39hd667e15_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.7.3=py39h27cfd23_1
- conda==4.11.0=py39h06a4308_0
- cryptography==36.0.0=py39h9ce1e76_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-64==2.35.1=h7274673_9
- libffi==3.3=he6710b0_2
- libgcc-ng==9.3.0=h5101ec6_17
- libgomp==9.3.0=h5101ec6_17
- libstdcxx-ng==9.3.0=hd4cf53a_17
- ncurses==6.3=h7f8727e_2
- openssl==1.1.1m=h7f8727e_0
- pip==21.2.4=py39h06a4308_0
- pycosat==0.6.3=py39h27cfd23_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==21.0.0=pyhd3eb1b0_1
- pysocks==1.7.1=py39h06a4308_0
- python==3.9.7=h12debd9_1
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h27cfd23_0
- setuptools==58.0.4=py39h06a4308_0
- six==1.16.0=pyhd3eb1b0_0
- sqlite==3.37.0=hc218d9a_0
- tk==8.6.11=h1ccaba5_0
- tqdm==4.62.3=pyhd3eb1b0_1
- tzdata==2021e=hda174b7_0
- urllib3==1.26.7=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.11=h7f8727e_4
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2
certifi pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.11.0-py39h06a4308_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.3-py39h27cfd23_1
cryptography pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1m-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-21.0.0-pyhd3eb1b0_1
pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.7-h12debd9_1
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-58.0.4-py39h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0
sqlite pkgs/main/linux-64::sqlite-3.37.0-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.62.3-pyhd3eb1b0_1
tzdata pkgs/main/noarch::tzdata-2021e-hda174b7_0
urllib3 pkgs/main/noarch::urllib3-1.26.7-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7f8727e_4
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
no change /home/bio16/miniconda3/condabin/conda
no change /home/bio16/miniconda3/bin/conda
no change /home/bio16/miniconda3/bin/conda-env
no change /home/bio16/miniconda3/bin/activate
no change /home/bio16/miniconda3/bin/deactivate
no change /home/bio16/miniconda3/etc/profile.d/conda.sh
no change /home/bio16/miniconda3/etc/fish/conf.d/conda.fish
no change /home/bio16/miniconda3/shell/condabin/Conda.psm1
no change /home/bio16/miniconda3/shell/condabin/conda-hook.ps1
no change /home/bio16/miniconda3/lib/python3.9/site-packages/xontrib/conda.xsh
no change /home/bio16/miniconda3/etc/profile.d/conda.csh
modified /home/bio16/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
bio16@VM-0-6-ubuntu:~/biosoft$ conda
conda: command not found
bio16@VM-0-6-ubuntu:~/biosoft$ source ~/.bashrc
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda
usage: conda [-h] [-V] command ...
conda is a tool for managing and deploying applications, environments and packages.
Options:
positional arguments:
command
clean Remove unused packages and caches.
compare Compare packages between conda environments.
config Modify configuration values in .condarc. This is modeled
after the git config command. Writes to the user .condarc
file (/home/bio16/.condarc) by default.
create Create a new conda environment from a list of specified
packages.
help Displays a list of available conda commands and their help
strings.
info Display information about current conda install.
init Initialize conda for shell interaction. [Experimental]
install Installs a list of packages into a specified conda
environment.
list List linked packages in a conda environment.
package Low-level conda package utility. (EXPERIMENTAL)
remove Remove a list of packages from a specified conda environment.
uninstall Alias for conda remove.
run Run an executable in a conda environment. [Experimental]
search Search for packages and display associated information. The
input is a MatchSpec, a query language for conda packages.
See examples below.
update Updates conda packages to the latest compatible version.
upgrade Alias for conda update.
optional arguments:
-h, --help Show this help message and exit.
-V, --version Show the conda version number and exit.
conda commands available from other packages:
content-trust
env
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
conda config --set show_channel_urls yes(base) bio16@VM-0-6-ubuntu:~/biosoft$ cos.bfsu.edu.cn/anaconda/cloud/conda-forge/
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda config --set show_channel_urls yes
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda list
# packages in environment at /home/bio16/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
_openmp_mutex 4.5 1_gnu defaults
brotlipy 0.7.0 py39h27cfd23_1003 defaults
ca-certificates 2021.10.26 h06a4308_2 defaults
certifi 2021.10.8 py39h06a4308_2 defaults
cffi 1.15.0 py39hd667e15_1 defaults
charset-normalizer 2.0.4 pyhd3eb1b0_0 defaults
conda 4.11.0 py39h06a4308_0 defaults
conda-content-trust 0.1.1 pyhd3eb1b0_0 defaults
conda-package-handling 1.7.3 py39h27cfd23_1 defaults
cryptography 36.0.0 py39h9ce1e76_0 defaults
idna 3.3 pyhd3eb1b0_0 defaults
ld_impl_linux-64 2.35.1 h7274673_9 defaults
libffi 3.3 he6710b0_2 defaults
libgcc-ng 9.3.0 h5101ec6_17 defaults
libgomp 9.3.0 h5101ec6_17 defaults
libstdcxx-ng 9.3.0 hd4cf53a_17 defaults
ncurses 6.3 h7f8727e_2 defaults
openssl 1.1.1m h7f8727e_0 defaults
pip 21.2.4 py39h06a4308_0 defaults
pycosat 0.6.3 py39h27cfd23_0 defaults
pycparser 2.21 pyhd3eb1b0_0 defaults
pyopenssl 21.0.0 pyhd3eb1b0_1 defaults
pysocks 1.7.1 py39h06a4308_0 defaults
python 3.9.7 h12debd9_1 defaults
readline 8.1.2 h7f8727e_1 defaults
requests 2.27.1 pyhd3eb1b0_0 defaults
ruamel_yaml 0.15.100 py39h27cfd23_0 defaults
setuptools 58.0.4 py39h06a4308_0 defaults
six 1.16.0 pyhd3eb1b0_0 defaults
sqlite 3.37.0 hc218d9a_0 defaults
tk 8.6.11 h1ccaba5_0 defaults
tqdm 4.62.3 pyhd3eb1b0_1 defaults
tzdata 2021e hda174b7_0 defaults
urllib3 1.26.7 pyhd3eb1b0_0 defaults
wheel 0.37.1 pyhd3eb1b0_0 defaults
xz 5.2.5 h7b6447c_0 defaults
yaml 0.2.5 h7b6447c_0 defaults
zlib 1.2.11 h7f8727e_4 defaults
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda install fastqc=0.11.7 -y
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.11.0
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/bio16/miniconda3
added / updated specs:
- fastqc=0.11.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.3.29 | h06a4308_0 117 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
certifi-2021.10.8 | py39h06a4308_2 151 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
conda-4.12.0 | py39h06a4308_0 14.5 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dbus-1.13.18 | hb2f20db_0 504 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
expat-2.4.4 | h295c915_0 169 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fastqc-0.11.7 | hdfd78af_7 9.6 MB https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
freetype-2.11.0 | h70c0345_0 618 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
glib-2.69.1 | h4ff587b_1 1.7 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libpng-1.6.37 | hbc83047_0 278 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxcb-1.14 | h7b6447c_0 505 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
openjdk-11.0.13 | h87a67e3_0 341.0 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
openssl-1.1.1n | h7f8727e_0 2.5 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pcre-8.45 | h295c915_0 207 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
perl-5.26.2 | h14c3975_0 10.5 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
------------------------------------------------------------
Total: 382.2 MB
The following NEW packages will be INSTALLED:
dbus anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
expat anaconda/pkgs/main/linux-64::expat-2.4.4-h295c915_0
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.11.7-hdfd78af_7
freetype anaconda/pkgs/main/linux-64::freetype-2.11.0-h70c0345_0
glib anaconda/pkgs/main/linux-64::glib-2.69.1-h4ff587b_1
libpng anaconda/pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
libxcb anaconda/pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
openjdk anaconda/pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0
pcre anaconda/pkgs/main/linux-64::pcre-8.45-h295c915_0
perl anaconda/pkgs/main/linux-64::perl-5.26.2-h14c3975_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2021.10.26~ --> anaconda/pkgs/main::ca-certificates-2022.3.29-h06a4308_0
conda pkgs/main::conda-4.11.0-py39h06a4308_0 --> anaconda/pkgs/main::conda-4.12.0-py39h06a4308_0
openssl pkgs/main::openssl-1.1.1m-h7f8727e_0 --> anaconda/pkgs/main::openssl-1.1.1n-h7f8727e_0
The following packages will be SUPERSEDED by a higher-priority channel:
certifi pkgs/main --> anaconda/pkgs/main
Downloading and Extracting Packages
openjdk-11.0.13 | 341.0 MB | ##################################### | 100%
perl-5.26.2 | 10.5 MB | ##################################### | 100%
dbus-1.13.18 | 504 KB | ##################################### | 100%
conda-4.12.0 | 14.5 MB | ##################################### | 100%
freetype-2.11.0 | 618 KB | ##################################### | 100%
libpng-1.6.37 | 278 KB | ##################################### | 100%
glib-2.69.1 | 1.7 MB | ##################################### | 100%
certifi-2021.10.8 | 151 KB | ##################################### | 100%
openssl-1.1.1n | 2.5 MB | ##################################### | 100%
libxcb-1.14 | 505 KB | ##################################### | 100%
expat-2.4.4 | 169 KB | ##################################### | 100%
pcre-8.45 | 207 KB | ##################################### | 100%
ca-certificates-2022 | 117 KB | ##################################### | 100%
fastqc-0.11.7 | 9.6 MB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) bio16@VM-0-6-ubuntu:~/biosoft$ ls
Miniconda3-py39_4.11.0-Linux-x86_64.sh
(base) bio16@VM-0-6-ubuntu:~/biosoft$ fastqc --help
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--casava Files come from raw casava output. Files in the same sample
group (differing only by the group number) will be analysed
as a set rather than individually. Sequences with the filter
flag set in the header will be excluded from the analysis.
Files must have the same names given to them by casava
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
--nano Files come from naopore sequences and are in fast5 format. In
this mode you can pass in directories to process and the program
will take in all fast5 files within those directories and produce
a single output file from the sequences found in all files.
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if fastqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch fastqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
--min_length Sets an artificial lower limit on the length of the sequence
to be shown in the report. As long as you set this to a value
greater or equal to your longest read length then this will be
the sequence length used to create your read groups. This can
be useful for making directly comaparable statistics from
datasets with somewhat variable read lengths.
-f --format Bypasses the normal sequence file format detection and
forces the program to use the specified format. Valid
formats are bam,sam,bam_mapped,sam_mapped and fastq
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-c Specifies a non-default file which contains the list of
--contaminants contaminants to screen overrepresented sequences against.
The file must contain sets of named contaminants in the
form name[tab]sequence. Lines prefixed with a hash will
be ignored.
-a Specifies a non-default file which contains the list of
--adapters adapter sequences which will be explicity searched against
the library. The file must contain sets of named adapters
in the form name[tab]sequence. Lines prefixed with a hash
will be ignored.
-l Specifies a non-default file which contains a set of criteria
--limits which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-k --kmers Specifies the length of Kmer to look for in the Kmer content
module. Specified Kmer length must be between 2 and 10. Default
length is 7 if not specified.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio16/miniconda3
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda create -n rna-seq python=3 fastqc trimmomatic
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio16/miniconda3/envs/rna-seq
added / updated specs:
- fastqc
- python=3
- trimmomatic
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | main 3 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
_openmp_mutex-4.5 | 1_gnu 22 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
bzip2-1.0.8 | h7b6447c_0 78 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
certifi-2020.6.20 | pyhd3eb1b0_3 155 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fastqc-0.11.9 | hdfd78af_1 9.7 MB https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono-2.37| hd3eb1b0_0 335 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fontconfig-2.13.1 | h6c09931_0 250 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
icu-58.2 | he6710b0_3 10.5 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ld_impl_linux-64-2.35.1 | h7274673_9 586 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libffi-3.3 | he6710b0_2 50 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libgcc-ng-9.3.0 | h5101ec6_17 4.8 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libgomp-9.3.0 | h5101ec6_17 311 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libstdcxx-ng-9.3.0 | hd4cf53a_17 3.1 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libuuid-1.0.3 | h7f8727e_2 17 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxml2-2.9.12 | h03d6c58_0 1.2 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ncurses-6.3 | h7f8727e_2 782 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
pip-21.2.4 | py310h06a4308_0 1.8 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
python-3.10.4 | h12debd9_0 24.2 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
readline-8.1.2 | h7f8727e_1 354 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
setuptools-61.2.0 | py310h06a4308_0 1019 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
sqlite-3.38.2 | hc218d9a_0 1.0 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
tk-8.6.11 | h1ccaba5_0 3.0 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
trimmomatic-0.39 | hdfd78af_2 144 KB https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
tzdata-2022a | hda174b7_0 109 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
wheel-0.37.1 | pyhd3eb1b0_0 33 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
xz-5.2.5 | h7b6447c_0 341 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
zlib-1.2.12 | h7f8727e_1 111 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
------------------------------------------------------------
Total: 63.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex anaconda/pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex anaconda/pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
bzip2 anaconda/pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
ca-certificates anaconda/pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_0
certifi anaconda/pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
dbus anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
expat anaconda/pkgs/main/linux-64::expat-2.4.4-h295c915_0
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.11.9-hdfd78af_1
font-ttf-dejavu-s~ anaconda/pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0
fontconfig anaconda/pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0
freetype anaconda/pkgs/main/linux-64::freetype-2.11.0-h70c0345_0
glib anaconda/pkgs/main/linux-64::glib-2.69.1-h4ff587b_1
icu anaconda/pkgs/main/linux-64::icu-58.2-he6710b0_3
ld_impl_linux-64 anaconda/pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi anaconda/pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng anaconda/pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp anaconda/pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libpng anaconda/pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
libstdcxx-ng anaconda/pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
libuuid anaconda/pkgs/main/linux-64::libuuid-1.0.3-h7f8727e_2
libxcb anaconda/pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
libxml2 anaconda/pkgs/main/linux-64::libxml2-2.9.12-h03d6c58_0
ncurses anaconda/pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openjdk anaconda/pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0
openssl anaconda/pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pcre anaconda/pkgs/main/linux-64::pcre-8.45-h295c915_0
perl anaconda/pkgs/main/linux-64::perl-5.26.2-h14c3975_0
pip anaconda/pkgs/main/linux-64::pip-21.2.4-py310h06a4308_0
python anaconda/pkgs/main/linux-64::python-3.10.4-h12debd9_0
readline anaconda/pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
setuptools anaconda/pkgs/main/linux-64::setuptools-61.2.0-py310h06a4308_0
sqlite anaconda/pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk anaconda/pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
trimmomatic anaconda/cloud/bioconda/noarch::trimmomatic-0.39-hdfd78af_2
tzdata anaconda/pkgs/main/noarch::tzdata-2022a-hda174b7_0
wheel anaconda/pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz anaconda/pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
zlib anaconda/pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1
Proceed ([y]/n)? y
Downloading and Extracting Packages
tk-8.6.11 | 3.0 MB | ##################################### | 100%
xz-5.2.5 | 341 KB | ##################################### | 100%
libgomp-9.3.0 | 311 KB | ##################################### | 100%
tzdata-2022a | 109 KB | ##################################### | 100%
pip-21.2.4 | 1.8 MB | ##################################### | 100%
zlib-1.2.12 | 111 KB | ##################################### | 100%
ld_impl_linux-64-2.3 | 586 KB | ##################################### | 100%
font-ttf-dejavu-sans | 335 KB | ##################################### | 100%
libuuid-1.0.3 | 17 KB | ##################################### | 100%
wheel-0.37.1 | 33 KB | ##################################### | 100%
bzip2-1.0.8 | 78 KB | ##################################### | 100%
libstdcxx-ng-9.3.0 | 3.1 MB | ##################################### | 100%
readline-8.1.2 | 354 KB | ##################################### | 100%
trimmomatic-0.39 | 144 KB | ##################################### | 100%
certifi-2020.6.20 | 155 KB | ##################################### | 100%
_openmp_mutex-4.5 | 22 KB | ##################################### | 100%
libxml2-2.9.12 | 1.2 MB | ##################################### | 100%
sqlite-3.38.2 | 1.0 MB | ##################################### | 100%
libgcc-ng-9.3.0 | 4.8 MB | ##################################### | 100%
fastqc-0.11.9 | 9.7 MB | ##################################### | 100%
icu-58.2 | 10.5 MB | ##################################### | 100%
setuptools-61.2.0 | 1019 KB | ##################################### | 100%
ncurses-6.3 | 782 KB | ##################################### | 100%
python-3.10.4 | 24.2 MB | ##################################### | 100%
_libgcc_mutex-0.1 | 3 KB | ##################################### | 100%
libffi-3.3 | 50 KB | ##################################### | 100%
fontconfig-2.13.1 | 250 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate rna-seq
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio16/miniconda3
rna-seq /home/bio16/miniconda3/envs/rna-seq
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda cativate rna-seq
CommandNotFoundError: No command 'conda cativate'.
Did you mean 'conda activate'?
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda activate rna-seq
(rna-seq) bio16@VM-0-6-ubuntu:~/biosoft$ fastqc
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
at java.desktop/java.awt.Window.<init>(Window.java:549)
at java.desktop/java.awt.Frame.<init>(Frame.java:423)
at java.desktop/java.awt.Frame.<init>(Frame.java:388)
at java.desktop/javax.swing.JFrame.<init>(JFrame.java:180)
at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338)
(rna-seq) bio16@VM-0-6-ubuntu:~/biosoft$ conda deactivate
(base) bio16@VM-0-6-ubuntu:~/biosoft$ conda remove fastqc -y
Collecting package metadata (repodata.json): | (base) bio16@VM-0-6-ubuntu:~/biosoft$
(base) bio16@VM-0-6-ubuntu:~/biosoft$ ls
Miniconda3-py39_4.11.0-Linux-x86_64.sh
(base) bio16@VM-0-6-ubuntu:~/biosoft$
