[khmer] Khmer install

[Michael R. Crusoe]

Yep, the command would be

pip install --no-clean khmer

You might need to use a fresh virtualenv.

There is a chance that your version of pip doesn't have that option. If so
I will find another way.

Thank you for your patience.
On Jan 29, 2014 9:15 AM, "Daniel Burkhardt" <burkhardt.d.b at gmail.com> wrote:

> Michael,
>
> Thank you for your quick response. Inside my virtualenv, I have pip
> version 1.1. When you suggest to add the --no-clean flag, are you referring
> to when I install khmer? It doesn't look like this is an option for pip.
>
> Inside of /env/ I have four directories: bin  include  lib  local
> bin contains the scripts for khmer and for the virtualenv
> include contains a link to python 2.7
> lib contains a directory of python 2.7
> local contains links to the 3 directories above (bin, include, lib)
>
> I cannot find a build/khmer directory anywhere on my system.
>
> Thanks again,
> Dan
>
> P.s. this is a full list of the contents of /env/bin:
>  abundance-dist.py         easy_install             load-into-counting.py
> abundance-dist-single.py  easy_install-2.7         make-initial-stoptags.py
> activate                  extract-paired-reads.py  merge-partitions.py
> activate.csh              extract-partitions.py    normalize-by-median.py
> activate.fish             filter-abund.py          partition-graph.py
> activate_this.py          filter-abund-single.py   pip
> annotate-partitions.py    filter-stoptags.py       pip-2.7
> count-median.py           find-knots.py            python
> count-overlap.py          interleave-reads.py      sample-reads-randomly.py
> do-partition.py           load-graph.py            split-paired-reads.py
>
>
>
>
> On Tue, Jan 28, 2014 at 5:19 PM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>
>> Thank you Dan for your email.
>>
>> pip, the tool we use for installing khmer and its dependencies, has gone
>> decided to break backwards compatibility with their version 1.5 release.
>>
>> Looks like you're using an earlier version which dies if you pass it an
>> argument it doesn't understand. I will update the docs to clarify the
>> situation.
>>
>> If your pip version is prior to 1.5 then install using `pip install
>> khmer`.
>>
>> If you're using pip version 1.5 or later then use: `pip install
>> --allow-external argparse khmer`
>>
>> I will also be updating the instructions on how to run the tests. Right
>> now the easiest way is to pass the '--no-clean' flag and to go into the
>> env/build/khmer directory where you can run `make tests`.
>>
>>
>>
>>
>> On Tue, Jan 28, 2014 at 3:26 PM, Daniel Burkhardt <
>> burkhardt.d.b at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I wasn't sure if I should email this address or the help listserv, but I
>>> figured it would be better to avoid emailing a bunch of people with a
>>> potentially novice question. My name is Daniel Burkhardt and I'm a research
>>> assistant fellow in the lab of Dr. Kristen DeAngelis at the University of
>>> Massachusetts, Amherst.
>>>
>>> The short question:
>>>
>>> I followed the instructions on the http://khmer.readthedocs.org/
>>> en/latest/install.html page, but I have no env/src directory. So I
>>> can't do the last step that says to run the tests under src/tests. I also
>>> do not have any of the sample files to try. I've done a system-wide search,
>>> but have no files with the pattern "stamps-reads" anywhere. My question is:
>>> what did I do wrong?
>>>
>>> Some background:
>>>
>>
>> <snip for privacy>
>>
>>
>>> I am running Ubuntu 12.04. I followed the instructions on the read the
>>> docs up through:
>>>
>>> pip install --allow-external argparse khmer
>>>
>>>
>>> but I can't find a src directory under my env directory. Also it seems
>>> that the --allow-external flag is outdated, and is no longer a valid option
>>> for pip. Attached is a .log file of pip's output. All of the scripts seem
>>> to have installed correctly, but I can't figure out why I have no tests
>>> directory or any sample files. Is this problem encountered often? I
>>> couldn't find any similar problem reports on the listserv archives. Did I
>>> miss something rudimentary? I would appreciate any insight you can offer.
>>>
>>> Thank you for your time,
>>> Dan
>>>
>>
>>
>>
>> --
>> Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
>>  @ the Genomics, Evolution, and Development lab; Michigan State U
>> http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe<http://twitter.com/biocrusoe>
>>
>
>
>
> --
> Daniel Burkhardt
> University of Massachusetts Amherst - Microbiology
> Cell: (978)-846-2197
>
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