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Issues with setting up conda - windows #140

Closed whalera1901 closed 3 years ago

whalera1901 commented 3 years ago

Hi,

I'm following along with the new edition of the handbook and am getting "conda: command not found" after setting everything up as the book says

I've tried redoing the steps several times, but the results are the same. I also tried typing in "bash miniconda-installer.sh -u" after it said that "my directory already exists" to see if that would fix anything (this was after my first few tries of following the book exactly). After trying out the -u option, it asked if I wanted to initialize it with "init" so I said yes. It then prompted me to close and open the terminal. I then tried going through the steps in the book again and still get the conda : command not found error.

Here is what my latest run looked like conda error

Sorry if anything is unclear as I'm completely new to this kind of stuff and thanks for your help in advance!

ialbert commented 3 years ago

you will need to close and reopen the terminal for the changes to take effect.

whalera1901 commented 3 years ago

Hi thanks for replying! I've actually already tried that and then reopened the terminal and it still has the conda: command not found error.

I've tried typing that in a few times actually after redoing all the steps with the same result.

On Wed, Feb 17, 2021, 7:57 AM Istvan Albert notifications@github.com wrote:

you will need to close and reopen the terminal for the changes to take effect

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-780538151, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMF7Q2DLZODI7WKXIEGTS7O4KJANCNFSM4XXTXD2A .

ialbert commented 3 years ago

This sounds like a path problem, you either are not in bash (perhaps you are running a different shell). What does this print?

echo $0

on my system it prints:

-bash

the way programs are found is governed by the so called PATH variable, there is a section in the handbook that explains the PATH.

https://www.biostarhandbook.com/bashpath.html

You shell is not seeing the conda location for some reason. It is either that the bash shell is wrong, or your have applied some steps incorrectly.

whalera1901 commented 3 years ago

Typing that in I see -bash [image: image.png] Does this mean the bash shell is fine and I applied some steps incorrectly? If I did the steps incorrectly, should I just go through them all again or is there something I need to undo since I've already tried going through them before?

Thank you for the help!

On Wed, Feb 17, 2021 at 11:12 AM Istvan Albert notifications@github.com wrote:

This sounds like a path problem, you either are not in bash (perhaps you are running a different shell). What does this print?

echo $0

on my system it prints:

-bash

the way programs are found is governed by the so called PATH variable, there is a section in the handbook that explains the PATH.

https://www.biostarhandbook.com/bashpath.html

You shell is not seeing the conda location for some reason. It is either that the bash shell is wrong, or your have applied some steps incorrectly.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-780668063, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMFYYJ67WE4N77VSDVSDS7PTITANCNFSM4XXTXD2A .

whalera1901 commented 3 years ago

Hi,

Sorry for another email so soon. This is what I'm getting as I'm trying to redo the "install conda" steps. Should I still proceed with the next step despite this result? [image: image.png]

Caroline Nitirahardjo

On Wed, Feb 17, 2021 at 3:19 PM Caroline Nitirahardjo cnitirah@kent.edu wrote:

Typing that in I see -bash [image: image.png] Does this mean the bash shell is fine and I applied some steps incorrectly? If I did the steps incorrectly, should I just go through them all again or is there something I need to undo since I've already tried going through them before?

Thank you for the help!

On Wed, Feb 17, 2021 at 11:12 AM Istvan Albert notifications@github.com wrote:

This sounds like a path problem, you either are not in bash (perhaps you are running a different shell). What does this print?

echo $0

on my system it prints:

-bash

the way programs are found is governed by the so called PATH variable, there is a section in the handbook that explains the PATH.

https://www.biostarhandbook.com/bashpath.html

You shell is not seeing the conda location for some reason. It is either that the bash shell is wrong, or your have applied some steps incorrectly.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-780668063, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMFYYJ67WE4N77VSDVSDS7PTITANCNFSM4XXTXD2A .

ialbert commented 3 years ago

please show the text,

no need to take screenshots, the terminal is text, you can highlight with your mouse and copy /paste it into the text box

whalera1901 commented 3 years ago

Opps sorry about that! Here is the text;

whalers1845@DESKTOP-IJ0BUL2:~$ URL=https:/ repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh whalers1845@DESKTOP-IJ0BUL2:~$ curl $URL > miniconda-installer.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 89.8M 100 89.8M 0 0 3890k 0 0:00:23 0:00:23 --:--:-- 4081k whalers1845@DESKTOP-IJ0BUL2:~$ bash miniconda-installer.sh -b ERROR: File or directory already exists: '/home/whalers1845/miniconda3' If you want to update an existing installation, use the -u option. whalers1845@DESKTOP-IJ0BUL2:~$ miniconda3/condabin/conda init no change /home/whalers1845/miniconda3/condabin/conda no change /home/whalers1845/miniconda3/bin/conda no change /home/whalers1845/miniconda3/bin/conda-env no change /home/whalers1845/miniconda3/bin/activate no change /home/whalers1845/miniconda3/bin/deactivate no change /home/whalers1845/miniconda3/etc/profile.d/conda.sh no change /home/whalers1845/miniconda3/etc/fish/conf.d/conda.fish no change /home/whalers1845/miniconda3/shell/condabin/Conda.psm1 no change /home/whalers1845/miniconda3/shell/condabin/conda-hook.ps1 no change /home/whalers1845/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh no change /home/whalers1845/miniconda3/etc/profile.d/conda.csh no change /home/whalers1845/.bashrc No action taken. whalers1845@DESKTOP-IJ0BUL2:~$

On Wed, Feb 17, 2021 at 3:57 PM Istvan Albert notifications@github.com wrote:

please show the text,

no need to take screenshots, the terminal is text, you can highlight with your mouse and copy /paste it into the text box

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-780847953, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMF6G763I7MWXJJMKGKDS7QUSHANCNFSM4XXTXD2A .

ialbert commented 3 years ago

I meant to the question I posed, what does:

echo $0

print, also since were are there what does 

echo $PATH

print?

whalera1901 commented 3 years ago

Here's what prints when I type echo $0 and echo $PATH

whalers1845@DESKTOP-IJ0BUL2:~$ echo $0 -bash whalers1845@DESKTOP-IJ0BUL2:~$ echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.UbuntuonWindows_2004.2020.812.0_x64__79rhkp1fndgsc:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/Program Files/AdoptOpenJDK/jdk-11.0.8.10-hotspot/bin:/mnt/c/Program Files/AdoptOpenJDK/jre-11.0.7.10-hotspot/bin:/mnt/c/Program Files/AdoptOpenJDK/jre-8.0.252.09-hotspot/bin:/mnt/c/Program Files (x86)/AdoptOpenJDK/jre-8.0.252.09-hotspot/bin:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Program Files/MEGA-X:/mnt/c/Users/Sean/AppData/Local/Microsoft/WindowsApps:/snap/bin whalers1845@DESKTOP-IJ0BUL2:~$

On Wed, Feb 17, 2021 at 4:28 PM Istvan Albert notifications@github.com wrote:

I meant to the question I posed, what does:

echo $0

print, also since were are there what does

echo $PATH

print?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-780866142, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMF35PQ43L22M6V3RW33S7QYI5ANCNFSM4XXTXD2A .

ialbert commented 3 years ago

this is a curious error, for whatever reason conda does not seem to have been added to the PATH. We'll try to track down why your conda init did not work/ What does this print:

cat ~/.bashrc | grep conda -A 5
whalera1901 commented 3 years ago

Hi sorry for the delay! Here is what I get

whalers1845@DESKTOP-IJ0BUL2:~$ cat ~/.bashrc | grep conda -A 5

>>> conda initialize >>>

!! Contents within this block are managed by 'conda init' !!

conda_setup="$('/home/whalers1845/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/home/whalers1845/miniconda3/etc/profile.d/conda.sh" ]; then . "/home/whalers1845/miniconda3/etc/profile.d/conda.sh" else export PATH="/home/whalers1845/miniconda3/bin:$PATH" fi fi unset conda_setup

<<< conda initialize <<<

whalers1845@DESKTOP-IJ0BUL2:~$ Caroline Nitirahardjo

On Wed, Feb 17, 2021 at 5:13 PM Istvan Albert notifications@github.com wrote:

this is a curious error, for whatever reason conda does not seem to have been added to the PATH. We'll try to track down while your conda init did not work/ What does this print:

cat ~/.bashrc | grep conda -A 5

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ialbert commented 3 years ago

everything is set up correctly, it should work

are you sure that you actually exit the application and not just minimize it when you close and reopen it

make sure to exit the whole thing

whalera1901 commented 3 years ago

I'm fairly certain...I exited and restarted my computer to make sure and I'm still getting this:

whalers1845@DESKTOP-IJ0BUL2:~$ conda conda: command not found whalers1845@DESKTOP-IJ0BUL2:~$

Sorry for the trouble!

On Thu, Feb 18, 2021 at 11:07 AM Istvan Albert notifications@github.com wrote:

everything is set up correctly, it should work

are you sure that you actually exit the application and not just minimize it when you close and reopen it

make sure to exit the whole thing

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ialbert commented 3 years ago

my next recommendation would be to reinstall conda:

# Reverts the changes to bash
~/miniconda3/condabin/conda init --reverse

# Removes all of miniconda
rm -rf miniconda3

close the terminal and reopen

# Rerun conda install
bash miniconda-installer.sh -b

# Rerun the init
~/miniconda3/condabin/conda init

now close the terminal and open it again (no need to restart the system)

let's see if conda can be run now

whalera1901 commented 3 years ago

Here's what I'm getting:

whalers1845@DESKTOP-IJ0BUL2:~$ ~/miniconda3/condabin/conda init --reverse no change /home/whalers1845/miniconda3/condabin/conda no change /home/whalers1845/miniconda3/bin/conda no change /home/whalers1845/miniconda3/bin/conda-env no change /home/whalers1845/miniconda3/bin/activate no change /home/whalers1845/miniconda3/bin/deactivate no change /home/whalers1845/miniconda3/etc/profile.d/conda.sh no change /home/whalers1845/miniconda3/etc/fish/conf.d/conda.fish no change /home/whalers1845/miniconda3/shell/condabin/Conda.psm1 no change /home/whalers1845/miniconda3/shell/condabin/conda-hook.ps1 no change /home/whalers1845/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh no change /home/whalers1845/miniconda3/etc/profile.d/conda.csh modified /home/whalers1845/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

whalers1845@DESKTOP-IJ0BUL2:~$ rm -rf miniconda3 whalers1845@DESKTOP-IJ0BUL2:~$

Second Part after re-opening

whalers1845@DESKTOP-IJ0BUL2:~$ bash miniconda-installer.sh -b PREFIX=/home/whalers1845/miniconda3 Unpacking payload ... Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/whalers1845/miniconda3

added / updated specs:

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003 ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0 certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 cffi pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2 chardet pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003 conda pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0 cryptography pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1 idna pkgs/main/noarch::idna-2.10-py_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0 pip pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pyopenssl pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1 pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0 python pkgs/main/linux-64::python-3.8.5-h7579374_1 readline pkgs/main/linux-64::readline-8.0-h7b6447c_0 requests pkgs/main/noarch::requests-2.24.0-py_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1 setuptools pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1 six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0 urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0 wheel pkgs/main/noarch::wheel-0.35.1-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-h7b6447c_3

Preparing transaction: done Executing transaction: done installation finished. whalers1845@DESKTOP-IJ0BUL2:~$ ~/miniconda3/condabin/conda init no change /home/whalers1845/miniconda3/condabin/conda no change /home/whalers1845/miniconda3/bin/conda no change /home/whalers1845/miniconda3/bin/conda-env no change /home/whalers1845/miniconda3/bin/activate no change /home/whalers1845/miniconda3/bin/deactivate no change /home/whalers1845/miniconda3/etc/profile.d/conda.sh no change /home/whalers1845/miniconda3/etc/fish/conf.d/conda.fish no change /home/whalers1845/miniconda3/shell/condabin/Conda.psm1 no change /home/whalers1845/miniconda3/shell/condabin/conda-hook.ps1 no change /home/whalers1845/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh no change /home/whalers1845/miniconda3/etc/profile.d/conda.csh modified /home/whalers1845/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

Third Part after re-opening

whalers1845@DESKTOP-IJ0BUL2:~$ conda conda: command not found

On Thu, Feb 18, 2021 at 11:57 AM Istvan Albert notifications@github.com wrote:

my next recommendation would be to reinstall conda:

Reverts the changes to bash

~/miniconda3/condabin/conda init --reverse

Removes all of miniconda

rm -rf miniconda3

close the terminal and reopen

Rerun conda install

bash miniconda-installer.sh -b

Rerun the init

~/miniconda3/condabin/conda init

now close the terminal and open it again (no need to restart the system)

let's see if conda can be run now

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ialbert commented 3 years ago

try running conda with full path and initialize environments that way, does that work? at any time that you would use conda type ~/miniconda3/condabin/conda

~/miniconda3/condabin/conda create --name bioinfo python=3.7

~/miniconda3/condabin/conda activate bioinfo

and so on

the problem is something odd, but also trivial in the end, the program is there just bash does not see it by default

whalera1901 commented 3 years ago

Here's how it looks. It doesn't look like it's working still to me:

whalers1845@DESKTOP-IJ0BUL2:~$ ~/miniconda3/condabin/conda create --name bioinfo python=3.7 Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/whalers1845/miniconda3/envs/bioinfo

added / updated specs:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2021.1.19  |       h06a4308_0         121 KB
certifi-2020.12.5          |   py37h06a4308_0         141 KB
openssl-1.1.1j             |       h27cfd23_0         2.5 MB
pip-20.3.3                 |   py37h06a4308_0         1.8 MB
python-3.7.9               |       h7579374_0        45.3 MB
readline-8.1               |       h27cfd23_0         362 KB
setuptools-52.0.0          |   py37h06a4308_0         710 KB
wheel-0.36.2               |     pyhd3eb1b0_0          33 KB
------------------------------------------------------------
                                       Total:        51.0 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main ca-certificates pkgs/main/linux-64::ca-certificates-2021.1.19-h06a4308_0 certifi pkgs/main/linux-64::certifi-2020.12.5-py37h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1j-h27cfd23_0 pip pkgs/main/linux-64::pip-20.3.3-py37h06a4308_0 python pkgs/main/linux-64::python-3.7.9-h7579374_0 readline pkgs/main/linux-64::readline-8.1-h27cfd23_0 setuptools pkgs/main/linux-64::setuptools-52.0.0-py37h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)? y

Downloading and Extracting Packages openssl-1.1.1j | 2.5 MB | ###################################################### | 100% certifi-2020.12.5 | 141 KB | ###################################################### | 100% wheel-0.36.2 | 33 KB | ###################################################### | 100% setuptools-52.0.0 | 710 KB | ###################################################### | 100% pip-20.3.3 | 1.8 MB | ###################################################### | 100% python-3.7.9 | 45.3 MB | ###################################################### | 100% ca-certificates-2021 | 121 KB | ###################################################### | 100% readline-8.1 | 362 KB | ###################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate bioinfo

#

To deactivate an active environment, use

#

$ conda deactivate

whalers1845@DESKTOP-IJ0BUL2:~$ conda activate bioinfo conda: command not found whalers1845@DESKTOP-IJ0BUL2:~$ conda conda: command not found whalers1845@DESKTOP-IJ0BUL2:~$

On Thu, Feb 18, 2021 at 12:27 PM Istvan Albert notifications@github.com wrote:

try running conda with full path and initialize environments that way, does that work?

~/miniconda3/condabin/conda create --name bioinfo python=3.7

the problem is something odd, but also trivial in the end, the program is there just bash does not see it by default

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-781508379, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMF2W7TI3KVEC27KBAL3S7VEXNANCNFSM4XXTXD2A .

ialbert commented 3 years ago

use ~/miniconda3/condabin/conda every time the instuctions say conda

in this case it would be:

~/miniconda3/condabin/conda activate bioinfo
whalera1901 commented 3 years ago

Hi,

I tried out what you typed but it still didn't work. However, I redid everything on a new laptop and it's working fine now. The things I did differently were: not change the display colours, skip the "make the prompt nicer" section, and ran "curl $URL > miniconda-installer.sh" a few times since it kept cancelling the process without downloading everything (did this until it reached 100%). Thanks for all your help!

Best, Caroline Nitirahardjo

On Thu, Feb 18, 2021 at 2:14 PM Istvan Albert notifications@github.com wrote:

use ~/miniconda3/condabin/conda every time the instuctions say conda

in this case it would be:

~/miniconda3/condabin/conda activate bioinfo

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/140#issuecomment-781573984, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANLQMF57D2S7DSN4YFVDSWTS7VRJBANCNFSM4XXTXD2A .

ialbert commented 3 years ago

glad it worked out.