Re: [galaxy-dev] conda installation fails

Hi, I second Marius here, I would not try to fix the miniconda installation, but rather fix the `tar` installation. This is not the original COS6.8 behaviour right? Ciao, Bjoern Am 19.04.2017 um 17:57 schrieb Matthias Bernt: > Dear list, > > Just found out that conda is not installing on our

Re: [galaxy-dev] conda installation fails

That's a little weird, I don't think relying on the system's LD_LIBRARY_PATH is good practice. Maybe you could try what was suggested in the last answer here: https://serverfault.com/questions/372987/centos-usr-local-lib-system-wide-ld-library-path . On 19 April 2017 at 17:57, Matthias Bernt

[galaxy-dev] conda installation fails

Dear list, Just found out that conda is not installing on our CentOS6.8 installation (might be related to earlier messages). The problem is that the shell script installing conda unsets the LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the installer). The command line

[galaxy-dev] GCC2107 Oral presentation abstract deadline extended to 29 April

Hello all, The deadline for submitting oral presentation abstracts for the 2017 Galaxy Community Conference has been extended to 29 April. And a reminder of some other GCC2017 deadlines: 15 May: Early registration

Re: [galaxy-dev] atlas version 3.10.2 installation error

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.

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] atlas version 3.10.2 installation error

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

Re: [galaxy-dev] Testing updated NCBI BLAST+ wrappers for version 2.5.0

This just went live on the main tool shed: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ You can report issues here or on GitHub at: https://github.com/peterjc/galaxy_blast/issues Thanks, Peter On Thu, Dec 8, 2016 at 11:35 AM, Peter Cock wrote: >