Hi,
I have a problem with the output of rcorrector which I would like to
wrap. The input are single-end or paired-end fastq file/s and the output
is the name (name of the input file) of the files plus ".cor.fq" so for
example:
input: sample_R1.fastq, sample_R2.fastq
output:
It's coming from the defaults channel, I didn't check if this is actually
working,
it may very well not be compatible with the remaining packages form
conda-forge.
AFAIK you can't specify packages to install via the regular conda commands
(though you can use pip in a conda environemnt to do this
Hello
I'm in the process of updating our local Galaxy tools to use conda dependency
resolution, and I've hit a snag with a tool that requires Python 2.7 along with
the Python 2.7-compatible version of Biopython 1.65.
I'd assumed that if I explicitly used the following in the "requirements"
This should actually work properly if you install the dependencies via
the Manage dependencies page in the admin menu or if you install the tool
via the tool shed.
This translates more or less to the following conda command:
```
$ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc
I stand corrected. Looking closer, there are conda packages
for both Python 2 and 3, e.g.
https://anaconda.org/conda-forge/biopython/files
However, in this case you're asking for an older Biopython
which has to date not been packaged in conda-forge or
bioconda, so I presume in Marius example it
Oh yeah - thanks, I can see them in the default channel which does have
far older versions of Biopython packaged - currently 1.65 is on page 5:
https://anaconda.org/anaconda/biopython/files?sort=basename_order=desc=5
Peter
On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek
Tricky, as I understand it the conda python packages are specific to
the conda version of Python - in this case Python 3 not 2.
It might actually be simpler to fix pal_finder/pal_filter.py to cope
with Python 3 - is the code online somewhere, I could probably cast an
eye over it.
Peter
On Mon,
Hi,
I could solve the problem with bzip. Now this part is working.
Cheers Jochen
On 02.03.2018 17:49, Nate Coraor wrote:
This occurs when bzip2 is installed from defaults instead of
conda-forge. If you have Conda >= 4.0 this shouldn't happen as long as
you install with the right channel
