I am running Qiime2-2019.10 on conda via our university’s cluster. I am trying to install breakaway following the instructions from this tutorial: Q2-breakaway: Community Tutorial
When I try to run the command “pip install git+https://github.com/statdivlab/q2-breakaway.git” I get the following error:
Collecting git+https://github.com/statdivlab/q2-breakaway.git
Cloning https://github.com/statdivlab/q2-breakaway.git to /tmp/pip-req-build-u35jj764
Running command git clone -q https://github.com/statdivlab/q2-breakaway.git /tmp/pip-req-build-u35jj764
ERROR: Command errored out with exit status 1:
command: /home/sthansen/miniconda/envs/qiime2-2019.10/bin/python -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-req-build-u35jj764/setup.py’"’"’; file=’"’"’/tmp/pip-req-build-u35jj764/setup.py’"’"’;f=getattr(tokenize, ‘"’"‘open’"’"’, open)(file);code=f.read().replace(’"’"’\r\n’"’"’, ‘"’"’\n’"’"’);f.close();exec(compile(code, file, ‘"’"‘exec’"’"’))’ egg_info --egg-base /tmp/pip-req-build-u35jj764/pip-egg-info
cwd: /tmp/pip-req-build-u35jj764/
Complete output (42 lines):
usage: git rev-list [OPTION] … [ – paths… ]
limiting output:
–max-count=nr
–max-age=epoch
–min-age=epoch
–sparse
–no-merges
–remove-empty
–all
–branches
–tags
–remotes
–stdin
–quiet
ordering output:
–topo-order
–date-order
–reverse
formatting output:
–parents
–children
–objects | --objects-edge
–unpacked
–header | --pretty
–abbrev=nr | --no-abbrev
–abbrev-commit
–left-right
special purpose:
–bisect
–bisect-vars
–bisect-all
Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-req-build-u35jj764/setup.py”, line 16, in
version=versioneer.get_version(),
File “/tmp/pip-req-build-u35jj764/versioneer.py”, line 1480, in get_version
return get_versions()[“version”]
File “/tmp/pip-req-build-u35jj764/versioneer.py”, line 1453, in get_versions
pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
File “/tmp/pip-req-build-u35jj764/versioneer.py”, line 1110, in git_pieces_from_vcs
pieces[“distance”] = int(count_out) # total number of commits
TypeError: int() argument must be a string, a bytes-like object or a number, not ‘NoneType’
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
I was able to successfully install breakaway on my own laptop. When I tried to run my first command however, I got this error (including some of the verbose info before error in case it’s helpful):
You have tibble installed!
You have magrittr installed!
Thank god! devtools is already available
Great! phyloseq is already available
Attempting to make phyloseq object…
[1] “otu_table”
attr(,“package”)
[1] “phyloseq”
Downloading GitHub repo adw96/[email protected]
sh: 1: /usr/bin/gzip: not found
sh: 1: /bin/gtar: not found
sh: 1: /usr/bin/gzip: not found
sh: 1: /bin/gtar: not found
Error: Failed to install ‘breakaway’ from GitHub:
error in running command
In addition: Warning messages:
1: In system(paste(TAR, “–version >”, tf, “2>&1”)) :
error in running command
2: In system(cmd) : error in running command
3: In utils::untar(tarfile, …) :
‘/usr/bin/gzip -dc ‘/tmp/RtmppKmxyD/file508a97d47a.tar.gz’ | /bin/gtar -xf ‘-’ -C ‘/tmp/RtmppKmxyD/remotes508b211edd’’ returned error code 127
4: In system(paste(TAR, “–version >”, tf, “2>&1”)) :
error in running command
Execution halted
Traceback (most recent call last):
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-487>”, line 2, in alpha
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_breakaway/_alphas.py”, line 54, in alpha
run_commands([cmd])
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_breakaway/_alphas.py”, line 37, in run_commands
subprocess.run(cmd, check=True)
File “/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_new_richness.R’, ‘/tmp/tmpfcppp6f7/table.tsv’, ‘/tmp/q2-AlphaDiversityFormat-t_fyoyf6’]’ returned non-zero exit status 1.
Plugin error from breakaway:
Command ‘[‘run_new_richness.R’, ‘/tmp/tmpfcppp6f7/table.tsv’, ‘/tmp/q2-AlphaDiversityFormat-t_fyoyf6’]’ returned non-zero exit status 1.
See above for debug info.
Any help would be appreciated!
