[khmer] Khmer install

[Michael R. Crusoe]

A git clone will indeed work. I will find a solution for other Ubuntu 12.04
users who are using the version that canonical ships.

FYI, you can upgrade pip for a single user with the following command:

pip install --upgrade --user pip

Cheers,
On Jan 30, 2014 8:16 AM, "Daniel Burkhardt" <burkhardt.d.b at gmail.com> wrote:

> So unfortunately there is no --no-clean option for pip version 1.1.
> However, it seems to me that the only issue is that the example files are
> in a src directory that pip is "cleaning up" as part of the installation. I
> have all the scripts that I should need for the tutorial, just not the
> sample data set. I think I might just grab the data directory from your git
> page and try to run things from there. This sounds like it should work,
> yeah?
>
> Thanks,
> Dan
>
>
> On Wed, Jan 29, 2014 at 10:23 AM, Michael R. Crusoe <mcrusoe at msu.edu>wrote:
>
>> 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
>>>
>>
>
>
> --
> Daniel Burkhardt
> University of Massachusetts Amherst - Microbiology
> Cell: (978)-846-2197
>
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