statdivlab / q2-breakaway Goto Github PK

View Code? Open in Web Editor NEW

8.0 8.0 4.0 208 KB

QIIME2 plug-in for breakaway

Makefile 0.25% Python 92.70% R 6.82% TeX 0.23%

q2-breakaway's People

Contributors

Stargazers

Watchers

Forkers

paulinetrinh fedarko shihuang047 khemlalnirmalkar

q2-breakaway's Issues

Sample names are modified in the alpha diversity output

Hi, and thanks for developing q2-breakaway!

The sample IDs in a dataset I'm looking at right now all start with numbers, so it looks like q2-breakaway is prefixing all of the IDs with an X. (From searching, it looks like this issue was briefly mentioned before here.) I think this is happening due to the call to read.table() here.

This doesn't cause any problems within q2-breakaway per se, but it's complicating the process of using the Breakaway output in other contexts in QIIME 2 (I'm currently trying to make a longitudinal plot that includes Breakaway's output, and since none of the sample IDs match up I need to export the alpha diversity, remove the starting Xs, and then re-import the alpha diversity). I imagine other people using this plugin will probably encounter these same problems eventually?

For whatever it's worth I remember running into this same issue in q2-aldex2, another plugin that communicates between QIIME 2 and R -- the solution @dgiguer had for that was using check.names=FALSE, although that was with read.delim() instead of read.table(). It looks like this option is also available for read.table(), but I don't know enough R to say for sure if that's a reasonable thing to do in this case...

In any case, thank you again for your work on this package! Looking forward to using it more :)

mvtnorm dependency

when removing mvtnorm dependency, change installation path back to adw96/breakaway repository

get rid of run_commands function

get rid of run_commands function.

replace

run_commands([cmd])

with

subprocess.run(cmd, check = True)

error in installation

> library("devtools"); options(unzip = "internal"); devtools::install_url("https://github.com/adw96/breakaway/archive/master.zip")
Downloading package from url: https://github.com/adw96/breakaway/archive/master.zip
Installing breakaway
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.6.tar.gz'
Content type 'application/x-gzip' length 710339 bytes (693 KB)
==================================================
downloaded 693 KB

sh: /bin/tar: No such file or directory
sh: /bin/tar: No such file or directory
Installation failed: error in running command
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.0.0.tar.gz'
Content type 'application/x-gzip' length 2847050 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

sh: /bin/tar: No such file or directory
sh: /bin/tar: No such file or directory
Installation failed: error in running command
trying URL 'https://cran.rstudio.com/src/contrib/MASS_7.3-50.tar.gz'
Content type 'application/x-gzip' length 487690 bytes (476 KB)
==================================================
downloaded 476 KB

sh: /bin/tar: No such file or directory
sh: /bin/tar: No such file or directory
Installation failed: error in running command
trying URL 'https://cran.rstudio.com/src/contrib/R.rsp_0.42.0.tar.gz'
Content type 'application/x-gzip' length 842386 bytes (822 KB)
==================================================
downloaded 822 KB

sh: /bin/tar: No such file or directory
sh: /bin/tar: No such file or directory
Installation failed: error in running command
'/Users/adwillis/anaconda3/envs/qiime2-2018.6/lib/R/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T/Rtmps7rMcS/devtoolscced2c35f023/breakaway-master'  \
  --library='/Users/adwillis/anaconda3/envs/qiime2-2018.6/lib/R/library'  \
  --install-tests 

* installing *source* package ‘breakaway’ ...
** R
** data
*** moving datasets to lazyload DB
** tests
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (breakaway)
Warning messages:
1: In utils::untar(src, exdir = target, compressed = "gzip") :
  ‘/bin/tar -xf '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/dplyr_0.7.6.tar.gz' -C '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/devtoolscced928a082'’ returned error code 127
2: In utils::untar(src, exdir = target, compressed = "gzip") :
  ‘/bin/tar -xf '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/ggplot2_3.0.0.tar.gz' -C '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/devtoolscced13210307'’ returned error code 127
3: In utils::untar(src, exdir = target, compressed = "gzip") :
  ‘/bin/tar -xf '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/MASS_7.3-50.tar.gz' -C '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/devtoolscced3d797a3b'’ returned error code 127
4: In utils::untar(src, exdir = target, compressed = "gzip") :
  ‘/bin/tar -xf '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/R.rsp_0.42.0.tar.gz' -C '/var/folders/j_/4kw5ygpn39d937k0tbcbr_lw0000gp/T//Rtmps7rMcS/devtoolscced68b8925f'’ returned error code 127
> 
>

R.rsp add to README

conda install -c conda-forge r-r.rsp

Plugin error when running breakaway in qiime2

I am trying to use breakaway to model estimated alpha diversity per suggestions from the qiime2 forum. Breakaway installs without error via conda and pip. However when I run the command
qiime breakaway alpha
--i-table table-dada2.qza
--o-alpha-diversity alpha_div/richness-better.qza
I get the following error message

Plugin error from breakaway:

Command '['run_new_richness.R', '/tmp/tmpbpkmn_rc/table.tsv', '/tmp/q2-AlphaDiversityFormat-iplggw0r']' returned non-zero exit status 1

looking at the log file it was looking for gtar and gzip
gzip was in /bin/gzip and not /usr/bin/gzip
I added gzip to /usr/bin but I still get the error...

Attached is the error log file.
breakaway_error_2.log

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.