Error source for downloading the latest version PhyloPhlAn2

[zwol...@gmail.com]

Dear all,

I have downloaded and installed PhyloPhlAn2 according to the weblink "https://bitbucket.org/nsegata/phylophlan/wiki/phylophlan2#markdown-header-requirements". But I found the source from the link "https://bitbucket.org/nsegata/phylophlan/get/default.tar.gz" was not PhyloPhlAn2 but should be PhyloPhlAn 1.0. So, could you please tell me the accurate source for downloading  the latest version PhyloPhlAn2. Thank you so much!

Cheers,

Zhigang

Please see below for looking for clues:

1. phylophlan.py but not phylophlan2.py were found in my installed directory.

2. Many new adding usages were not found. 

>Phython phylophlan.py -h

>you can see 

"PhyloPhlAn version 0.99 (8 May 2013)"

usage: phylophlan.py [-h] [-i] [-u] [-t] [--tax_test TAX_TEST] [-c]

                     [--cleanall] [--nproc N] [-v]

                     [PROJECT NAME]

[Francesco Asnicar]

Dear Zhigang,

Thanks for trying PhyloPhlAn v2. The documentation at that point assumes that we have published PhyloPhlAn v2 in the main branch of the repository, which is not yet the case.

To get PhyloPhlAn v2 from the repository you can clone it:
 $ hg clone https://bitbucket.org/nsegata/phylophlan

And then switch to the "dev" branch:

 $ hg update dev

At this point you should get the latest PhyloPhlAn v2 that we have in Bitbucket.

Please, let me know if something is not clear.

Many thanks,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/0360928b-b5ce-489b-a651-e5049b05bb7e%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[zhigang zhang]

Dear  Francesco,

Thank you very much for your support. It is very clear. Yes, I got it.

Cheers,

Zhigang

Francesco Asnicar <francesc...@gmail.com> 于2018年9月27日周四 下午2:55写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CAORa9gpDd9eJVdcJhrq5C0z9J8h83u398RpnbDqcnQwNx3w5CQ%40mail.gmail.com.

[zhigang zhang]

Dear  Francesco,

At present, I want to insert my newly sequenced genomes into the referred microbial tree of life built by your platform using PhyloPhlAn v2.0. To do it, I must download 4000 referred genomes & proteomes according to your tutorial "Download the 4000 (?) genomes/proteomes for this tutorial from here (put link or script to download genomes). " However, I found the source link was not existed. So, could you please tell me an active web link for download those data sets? Thank you very much for this help.

Bests,

Zhigang

 

Francesco Asnicar <francesc...@gmail.com> 于2018年9月27日周四 下午2:55写道：

Dear Zhigang,

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CAORa9gpDd9eJVdcJhrq5C0z9J8h83u398RpnbDqcnQwNx3w5CQ%40mail.gmail.com.

[zhigang zhang]

Dear  Francesco,

Thank you very much for your response. I have resolved this question about downloading reference database.

Cheers,

Zhigang

Francesco Asnicar <francesc...@gmail.com> 于2018年9月27日周四 下午2:55写道：

Dear Zhigang,

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CAORa9gpDd9eJVdcJhrq5C0z9J8h83u398RpnbDqcnQwNx3w5CQ%40mail.gmail.com.