Good news: With Marius' help Biopython 1.67 should be in bioconda
shortly, https://github.com/bioconda/bioconda-recipes/pull/4462
That means any Galaxy package using Biopython needing/wanting
to work under both the legacy XML packaging system and bioconda
will be able to point at Biopython 1.67.
I've emailed the rest of the IUC for their input - adding the old versions
in bioconda should work, or adding the recent Biopython releases as
packages on the Tool Shed.
For blast_rbh just need a semi-recent Biopython available in both systems
(until everyone moves over to bioconda - we've not
Dear Peter,
thanks. Just for understanding: Why not just change the biopython
dependency from 1.67 to 1.69, if this is the one available in bioconda.
blast_rbh seems to use only the SeqIO fasta parser and writer. This
should be no problem.
But I guess that for older versions of blast_rbh
Just lucky timing, could you try blast_rbh v0.1.11,
https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9069586
For BLAST+ this ought to work with either bioconda, or the legacy XML
based packages, as both have BLAST+ 2.5.0.
However, it looks like bioconda only has Biopython 1.68 and
Dear Peter,
thanks for the info. Would be great to get the update, but since I have
a method that is working for the moment there is no need to hurry.
Best,
Matthias
On 19.04.2017 12:57, Peter Cock wrote:
Oh right - I've just been updating ncbi_blast_plus this morning
to transition to
Oh right - I've just been updating ncbi_blast_plus this morning
to transition to BLAST+ 2.5.0 via either bioconda or the older
legacy Tool Shed.
I can try to update blast_rbh next, which may solve this by
letting you use bioconda.
Peter
On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt
Dear Marius,
thanks again for the help. I'm trying to install blast_rbh (owner is
peterjc). The dependencies look as follows:
blast_rbh
- biopython
- package_biopython_1_64
- package_numpy_1_8
- package_atlas_3_10
- blast
- package_blast_plus_2_2_31
- blast+
With
