qiime/qiime-deploy-conf

configuration files to be used with the qiime-deploy packages

QIIME: Quantitative Insights Into Microbial Ecology

QIIME 2 has succeeded QIIME 1 as of January 1, 2018. QIIME 1 is no longer officially supported, as our development and support efforts are now focused entirely on QIIME 2. For more information about what this means, see our blog post: QIIME 2 has succeeded QIIME 1.

QIIME 1 users should transition from QIIME 1 to QIIME 2. If you're new to QIIME, you should start by learning QIIME 2, not QIIME 1.

The QIIME 1 website can be found at http://www.qiime.org. For related software projects and data, see biocore.

qiime-deploy-conf's Issues

remove pplacer and parsinsert

we dropped insert_seqs_into_tree.py so these aren't dependencies anymore.

add installation of oligotyping

Though this isn't used directly by QIIME, it's pip-installable and likely of use to QIIME VM users. I think we should add this.

http://oligotyping.org/2012/05/11/oligotyping-pipeline-explained/

@jairideout, could you take care of this before QIIME 1.9.0?

Update QIIME 1.5.0 config to point to GitHub

Once the QIIME release files are copied to GitHub from SourceForge, the 1.5.0 config needs to be updated to download the file from GitHub.

Remove gtools and klar

(python27)06:51:29 software$ find qiime/qiime/. -type f -exec egrep -H "gtools|klar" {} \;
(python27)06:51:44 software$ find pycogent/cogent/. -type f -exec egrep -H "gtools|klar" {} \;

They don't appear to be in use anywhere

should we have a qiime-dependencies.conf?

I'm setting up a new server that we'll be using for a lot of QIIME analyses in my lab. One thing I'd like to be able to do is have all of the dependencies (basically, everything except QIIME itself) installed in location that is accessible system-wide, and then individual users put the QIIME git repo under their user account so they can work on their own branches, etc.

I could see doing this if we had a qiime-deploy that didn't install QIIME. Users could then add something like source /qiime_software/activate.sh to their .bash_profile, and add their QIIME fork to PATH and PYTHONPATH, or whatever their preferred strategy is for pointing to QIIME. If the user is also a PyCogent or BIOM developer, they could point to versions of those repos under their user account also. Or maybe a better strategy is to just use the dev conf file, and let the user override PATH and PYTHONPATH to point to any repos that they're a developer on?

@wasade, @jrrideout, and @pdmars: do you have thoughts about how to handle this?

1.8 conf refers to pplacer alpha14 but downloaded version is alpha15

As per the title, it appears pplacer has recently been updated.

add new version of AmpliconNoise

Currently waiting on release of the new version.

ViennaRNA link has moved

the correct link is now
http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz

Update QIIME conf file to not pull qiime_test_data

Now that qiime_test_data has been merged into the main QIIME repo, the QIIME 1.6.0-dev conf file needs to be updated so that it doesn't pull from the old repo anymore. This old repo will be left in place so that existing links (e.g. on the QIIME blog) don't break, and @gregcaporaso will be updating the README to point users to the new location.

python 2.7.3

Should we add python 2.7.3 in the dev version?

Add HDF5 libraries for the QIIME installation

install mafft in VirtualBox

Imported from qiime issue 221: biocore/qiime#221

The plan is to port this issue to PyCogent once it is in GitHub as the current mafft supported version (v6.602) is old.

need 12_10 version of greengenes in 1.5.0-dev

Currently still pulling 4feb2011 Greengenes. The relevant URL is:

ftp://greengenes.microbio.me/greengenes_release/gg_12_10/gg_12_10_otus.tar.gz

infernal path is incorrect

The address found in the 1.9.1 conf file for infernal is no longer accurate.

Old address: ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz
Current address: http://eddylab.org/software/infernal/infernal-1.0.2.tar.gz

add PATH=$SGE_ROOT/bin/linux-x64:$PATH to env for ipython

While doing the EC2 AMI release for 1.7.0 we realized that we need to add PATH=$SGE_ROOT/bin/linux-x64:$PATH to the env for ipython notebook to work. This should be part of the deploy.

Wrong installation link

Hi Meren,

I'm excited to start my first oligotyping analysis with your software! Just fyi, the link to the installation instructions on your tutorial "Oligotyping pipeline explained" is incorrect. Other users may be having difficulty locating the install instructions as well.

Best,
Michelle

v1.8.0 [R] package failure

FYI, on Centos 6, the R configuration and installation fails unless we need to add:

"autoconf-configure-options: --without-x"

Here is the full entry:

[r]
version: 3.0.2
build-type: autoconf
release-file-name: R-3.0.2.tar.gz
release-location: http://cran.case.edu/src/base/R-3/R-3.0.2.tar.gz
relative-directory-add-to-path: bin
autoconf-configure-options: --without-x
autoconf-make-options: -j4

Cheers,
-E

1.7 and 1.8 configuration files have links to the beast

the configuration files for 1.7 and 1.8 have links to thebeast which are dead. the links should be updated or we need to inform users that those deploys will not work.

R install should enable shared libraries

I'm not aware of a reason to avoid this, and it reduces deployment burden for others as R is a common package for a lot of other platforms. This was discussed on the forum here, but I disagree that enabling shared libraries as a compilation mod is a concern for QIIME (if it is, then that is a concern for R in general...)

upgrade R version to 3.0.1 in QIIME config

The R version should be upgraded from 2.12.0 to 3.0.1 in the QIIME 1.7.0-dev config file. See this issue for more details.

SQLAlchemy link is dead

The current SQLAlchemy link used in the QIIME 1.8.0 conf is dead and should be replaced with https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.7.1.tar.gz

ability to set paths when deploying auto-deploy script

It would be really nice to be able to define the path that is used for the .bashrc file during auto-deploy. (and the set up of the bashrc) as an option in the app_deploy.py script. I have run into problems on compy tracking down the paths, which is I think primarily related to python installation pointing to /home/lapa4025 instead of the new /Users/lapa4025. I reinstalling python to fix this. Might not be a general problem, but being able to specify the path (e.g. to $HOME) may solve future problems. This sort of ability was also requested by the IT person setting up Qiime on virtual machines for the ACAD workshop.

Thanks!

update to ampliconnoise 1.27

Wrong version of mothur in qiime-1.5.0-dev/qiime.conf

The link to download mothur in qiime-1.5.0-dev/qiime.conf downloads mothur 1.27 instead of 1.25.

I can't find a precompiled 1.25 binary on the mothur website, and I wasn't able to add a target the config file to build mothur from source because it looks like the build requires manual editing of the makefile.

should we merge the qiime-deploy-conf repo with the qiime-deploy repo?

Should we merge the qiime-deploy-conf repo with the qiime-deploy repo?

It'll be one less repo to keep track of and I'm not sure what the benefits are of keeping these two separate. Often times I'll have to submit two pull requests and make sure that they both get merged at the same time, which is a pain. Also, it'll be one less repo that users have to clone in order to use the tool.

Are there any objections to this change? If not, I'm happy to work on this.

Permissions set differently on different directories in /home/ubuntu/qiime_software/

Not a major issue, but I noticed that the permissions on these directories in the EC2 instance:

fasttree-2.1.3-release
cytoscape-2.7.0-release 
pplacer-1.1-release 
parsinsert-1.0.4-release

Have permission 700. This means that other users can't access things like the FastTree executable, even if

/home/ubuntu/qiime_software/fasttree-2.1.3-release/

is in their $PATH.

I came across this because I have a mutli-user cluster set up for my class this semester on AWS (the StarCluster CreateUsers plugin is awesome, btw), but I'm having everyone share a single QIIME install. Running FastTree failed as another user on the system.