Singularity and panEDTA

[joannarifkin]

Hi there,

Thanks for developing EDTA - it's great! And I'm excited to run panEDTA - I've already successfully run EDTA on 10 related species.

Apologies if this is a silly question, but I'm having trouble figuring out the interface of panEDTA and the EDTA singularity container. I run EDTA from the singularity container (singularity exec ~/EDTA.sif EDTA.pl), but I can't figure out where in the container to execute panEDTA from, and when I execute the panEDTA script from outside the container, it cannot find EDTA.pl:

Can't open perl script "~/util/count_base.pl": No such file or directory Can't open perl script "~/EDTA.pl": No such file or directory ERROR: Initial EDTA failed for Ler.test.fa

I tried re-downloading panEDTA.sh into the singularity EDTA directory from within the singularity shell, but it said it was a read-only file system. What am I missing?

Thanks again!

Joanna

[oushujun]

Hi Joanna,

I have not tested panEDTA in singularity yet. Can you please let me know which singulartiy verison of EDTA you are using?

Thanks, Shujun

[joannarifkin]

Hi Shujun,

Thanks for getting back to me so quickly!

I've been using version 2.0.0. I'm working on several plant genomes in the Brassicaceae, some small, some large and TE-rich.

Thanks again!

Joanna

On Wed, May 24, 2023 at 2:23 PM Shujun Ou @.***> wrote:

Hi Joanna,

I have not tested panEDTA in singularity yet. Can you please let me know which singulartiy verison of EDTA you are using?

Thanks, Shujun

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/363#issuecomment-1561735115, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFPL6CW3YWLSLM7XVULOJADXHZG2TANCNFSM6AAAAAAYNTDDS4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Joanna Rifkin PhD Postdoctoral fellow at the University of Michigan

[joannarifkin]

Hi again Shujun,

Any thoughts about running panEDTA via Singularity?

Thanks so much for all your help!

Joanna

On Wed, May 24, 2023 at 3:34 PM Joanna R. @.***> wrote:

Hi Shujun,

Thanks for getting back to me so quickly!

I've been using version 2.0.0. I'm working on several plant genomes in the Brassicaceae, some small, some large and TE-rich.

Thanks again!

Joanna

On Wed, May 24, 2023 at 2:23 PM Shujun Ou @.***> wrote:

Hi Joanna,

I have not tested panEDTA in singularity yet. Can you please let me know which singulartiy verison of EDTA you are using?

Thanks, Shujun

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/363#issuecomment-1561735115, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFPL6CW3YWLSLM7XVULOJADXHZG2TANCNFSM6AAAAAAYNTDDS4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Joanna Rifkin PhD Postdoctoral fellow at the University of Michigan

-- Joanna Rifkin PhD Postdoctoral fellow at the University of Michigan

[joannarifkin]

Hi again,

Thanks again for your awesome program! Any sense on whether panEDTA is likely to be working with Singularity soon or whether I should find a workaround? I can get help from the IT folks at the university if I need to.

Thanks!

Joanna

[oushujun]

Hi Joanna,

Sorry I have been very slow on this. I need to learn more about the issue. Did you pull the singularity version from this approach? singularity pull EDTA.sif docker://oushujun/edta:<tag> This was the version I created before migrating to a new Apple computer with the M1 ARM chip, and the machine is giving me a hardtime in rebuilding singularity images and that's why it has not been updated.

I will try to solve this in the summer, but I recommend reaching out to your IT support to install the conda version, which is newer than the singularity version.

Best wishes, Shujun

[joannarifkin]

Hi Shujun,

Thanks, that's very helpful! I'll do that.

Thank you again!

Joanna

On Tue, Jun 27, 2023 at 5:21 PM Shujun Ou @.***> wrote:

Hi Joanna,

Sorry I have been very slow on this. I need to learn more about the issue. Did you pull the singularity version from this approach? singularity pull EDTA.sif docker://oushujun/edta: This was the version I created before migrating to a new Apple computer with the M1 ARM chip, and the machine is giving me a hardtime in rebuilding singularity images and that's why it has not been updated.

I will try to solve this in the summer, but I recommend reaching out to your IT support to install the conda version, which is newer than the singularity version.

Best wishes, Shujun

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/363#issuecomment-1610236676, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFPL6CX6F7UN76UNRX6RPRDXNNFEPANCNFSM6AAAAAAYNTDDS4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Joanna Rifkin PhD Postdoctoral fellow at the University of Michigan

[philippbayer]

Here's a workaround; the Docker image of v2.0.0 is 2 years old so older than panEDTA.sh, I believe?

singularity pull EDTA.sif docker://oushujun/edta:2.0.0

You can check whether it's included:

singularity run EDTA.sif bash
ls /EDTA
exit

and you can see it's not there:

Dockerfile  EDTA.yml          EDTA_raw.pl  README.md  database     lib-test.pl  util
EDTA.pl     EDTA_processI.pl  LICENSE      bin        development  test

Here's the workaround:

wget https://raw.githubusercontent.com/oushujun/EDTA/master/panEDTA.sh

Edit the panEDTA.sh file: replace this line

path=$(dirname "$0") #program path

by

path="/EDTA"

Then you might be able to run it, at least it worked in my small test:

singularity run EDTA.sif bash panEDTA.sh -g genomes.txt -c genome.cds.fa

[joannarifkin]

Thanks so much!

I ended up just solving this by switching to the conda install, which seems to be working well.

Thanks again!

Joanna

On Tue, Sep 12, 2023 at 2:08 AM Philipp Bayer @.***> wrote:

Here's a workaround; the Docker image of v2.0.0 is 2 years old so older than panEDTA.sh, I believe?

singularity pull EDTA.sif docker://oushujun/edta:2.0.0

You can check whether it's included:

singularity run EDTA.sif bash ls /EDTA exit

and you can see it's not there:

Dockerfile EDTA.yml EDTA_raw.pl README.md database lib-test.pl util EDTA.pl EDTA_processI.pl LICENSE bin development test

Here's the workaround:

wget https://raw.githubusercontent.com/oushujun/EDTA/master/panEDTA.sh

Edit the panEDTA.sh file: replace this line

path=$(dirname "$0") #program path

by

path="/EDTA"

Then you might be able to run it, at least it worked in my small test:

singularity run EDTA.sif bash panEDTA.sh -g genomes.txt -c genome.cds.fa

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/363#issuecomment-1715046463, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFPL6CTKITWJGAW4CRX67S3XZ736RANCNFSM6AAAAAAYNTDDS4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Joanna Rifkin PhD they/them Computational biologist

[oushujun]

@philippbayer Thanks for the creative alternative! I am sure people will benefit from it.

Shujun