modkit: command not found

[gsukrit]

Hi,

I downloaded the modkit repo from the given instructions and added it to the PATH. Trying to run modkit pileup but throws an error saying command not found.

[sklages]

What did you exactly do to install modkit, which directory have you added to the $PATH and what exact error message do you get? Linux?

[gsukrit]

Hi,

I installed modkit using the following commands:

git clone https://github.com/nanoporetech/modkit.gitcd modkit cargo install --path .

I am getting the following error upon running the executable:

[image: image.png]

Thanks for the assistance.

Regards,

Sukriti

On Tue, May 30, 2023 at 3:07 PM sklages @.***> wrote:

What did you exactly do to install modkit, which directory have you added to the $PATH and what exact error message do you get? Linux?

— Reply to this email directly, view it on GitHub https://github.com/nanoporetech/modkit/issues/23#issuecomment-1568116153, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOY3FGI23IBKZUJY6AKPEDXIW5VPANCNFSM6AAAAAAYSWHZKE . You are receiving this because you authored the thread.Message ID: @.***>

-- Sukriti Gujarati PhD Scholar, Department of Biological Sciences, BITS Pilani, Rajasthan, India

-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.

[sklages]

I cannot see the image.

[ArtRand]

You may need to cd into the cloned repository. After cargo install --path ., at the end of the install process (downloading the dependencies and compiling), do you see a few lines similar to this?

   Compiling mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit)
    Finished release [optimized] target(s) in 58.82s
  Installing /Users/art.rand/.cargo/bin/modkit
   Installed package `mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit)` (executable `modkit`)

[gsukrit]

Hi,

Attaching a screenshot after the installation of modkit:

[image: image.png]

Hope it helps. Please let me know how can i proceed further.

Thanks, Sukriti

On Tue, May 30, 2023 at 7:27 PM Arthur Rand @.***> wrote:

You may need to cd into the cloned repository. After cargo install --path ., at thee end of the install process (downloading the dependencies and compiling), do you see a few lines similar to this?

Compiling mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit) Finished release [optimized] target(s) in 58.82s Installing /Users/art.rand/.cargo/bin/modkit Installed package mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit) (executable modkit)

— Reply to this email directly, view it on GitHub https://github.com/nanoporetech/modkit/issues/23#issuecomment-1568483987, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOY3FFPWDE3PIVD74KWQ7LXIX4FFANCNFSM6AAAAAAYSWHZKE . You are receiving this because you authored the thread.Message ID: @.***>

-- Sukriti Gujarati PhD Scholar, Department of Biological Sciences, BITS Pilani, Rajasthan, India

-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.

[gsukrit]

Hi,

Attaching a screenshot after installation. Hope it helps. Please let me know how to proceed further. [image: image.png]

Thanks, Sukriti

On Tue, May 30, 2023 at 7:27 PM Arthur Rand @.***> wrote:

You may need to cd into the cloned repository. After cargo install --path ., at thee end of the install process (downloading the dependencies and compiling), do you see a few lines similar to this?

Compiling mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit) Finished release [optimized] target(s) in 58.82s Installing /Users/art.rand/.cargo/bin/modkit Installed package mod_kit v0.1.7 (/Users/art.rand/projects/github/modkit) (executable modkit)

— Reply to this email directly, view it on GitHub https://github.com/nanoporetech/modkit/issues/23#issuecomment-1568483987, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOY3FFPWDE3PIVD74KWQ7LXIX4FFANCNFSM6AAAAAAYSWHZKE . You are receiving this because you authored the thread.Message ID: @.***>

-- Sukriti Gujarati PhD Scholar, Department of Biological Sciences, BITS Pilani, Rajasthan, India

-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.

[ArtRand]

@gsukrit I still cannot see the images. Perhaps try and upload them via the github website or cut-and-paste the actual text?

[sklages]

@gsukrit - it is probably better to use the github website - here https://github.com/nanoporetech/modkit/issues/23 - to create/comment issues as you can instantly see how your post looks like ..

[ArtRand]

@gsukrit any update here?

[ArtRand]

@gsukrit ,

Closing due to inactivity, feel free to re-open if you have any more questions.