No Access to Bitbucket

[Jie Liu]

Hi, I tried to go to the PhlyophlAn site on Bitbucket from the link https://bitbucket.org/nsegata/phylophlan. But every time, I got the message as below "We can't let you see this page".

I tried to log in with my account and sign up a new account, but still have to access to this site.

Is there a special code needed for accessing this site?

Thank you!

Jie

We can't let you see this page

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[Francesco Asnicar]

Hello Jie, 

Due to the dismiss of mercurial in Bitbucket, we decided to move all our software to Github. 

You can find the PhyloPhlAn repository here:

https://github.com/biobakery/phylophlan

We'll make some announcements about this change later this week / early next week, sorry that you couldn't find the repo. 

Many thanks, 

Francesco 

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[Jie Liu]

Thanks for your quick reply! Will all the issues be also move to Github? I did installed the PhyloPhlAn according to the Github instructions (Conda install).

But have some problems to run it on a HPC server. I couldn't access to the issues to figure out where is wrong.

 It kept giving this error message..

[e] Command '['FastTree']' returned non-zero exit status 1.

[e] program not installed or not present in the system path

    command_line: FastTree

           stdin: None

          stdout: None

             env: {'SLURM_NODELIST': 'tiger-h20d1', 'SLURM_JOB_NAME': 'runPhylophlan3-JL-test.sh', 'MANPATH': '/usr/share.......

However, when I echo fasttree, it show the fast tree was installed :  fasttree 2.1.10 h14c3975_3 bioconda

Could you please give any help?

Thank you so much!!

On Tuesday, April 7, 2020 at 1:23:34 AM UTC-4, francescoasnicar wrote:

Hello Jie, 

Due to the dismiss of mercurial in Bitbucket, we decided to move all our software to Github. 

You can find the PhyloPhlAn repository here:

https://github.com/biobakery/phylophlan

We'll make some announcements about this change later this week / early next week, sorry that you couldn't find the repo. 

Many thanks, 

Francesco 

On Tue, Apr 7, 2020, 12:58 AM Jie Liu <jiel...@gmail.com> wrote:

Hi, I tried to go to the PhlyophlAn site on Bitbucket from the link https://bitbucket.org/nsegata/phylophlan. But every time, I got the message as below "We can't let you see this page".

I tried to log in with my account and sign up a new account, but still have to access to this site.

Is there a special code needed for accessing this site?

Thank you!

Jie

We can't let you see this page

To access this page, you may need to log in with another account. You can also return to the previous page or go back to your dashboard.

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[Francesco Asnicar]

Hello Jie, 

Yes, the issues tracker in use now is the one of the GitHub repo: https://github.com/biobakery/phylophlan/issues

About your error, I think it might be due to the environment when working on an HPC infrastructure, which in the past gave similar problems.

I'm considering to update the check_dependencies function to solve this issue. However, a quick workaround just for now (until the new release where this will be fixed) is that you clone the PhyloPhlAn repository and edit the phylophlan.py script commenting line 3203 by adding a "#" at the beginning.

You can then use PhyloPhlAn by running the scripts or install it using the "python setup.py install" command.

Many thanks,

Francesco

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[Jie Liu]

Thanks Francesco, 

I tried to # the comments, but it didn't solve the errors. I did install it using Bioconda, which seems an easy install according to the manual. For this, do I still need to run setup.py install to get installation completed? Or I should re-install the pipeline using the repo install method and do this trick. 

Best,

Jie

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[Francesco Asnicar]

Hi Jie, 

With the conda installation it is a bit more tricky to comment that line.

You can try that by (1) cloning the repo, (2) comment the line, and (3) run phylophlan by executing the scripts you find in the repo.

I'm currently working on those fixes, but I can't give you an eta about when they will be available in the Bioconda package.

Many thanks,

Francesco

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