statdivlab / q2-breakaway Goto Github PK
View Code? Open in Web Editor NEWQIIME2 plug-in for breakaway
QIIME2 plug-in for breakaway
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 X
s, 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 :)
when removing mvtnorm dependency, change installation path back to adw96/breakaway repository
get rid of run_commands function.
replace
run_commands([cmd])
with
subprocess.run(cmd, check = True)
> 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
>
>
conda install -c conda-forge r-r.rsp
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
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.