Repository with installation scripts and environment definitions for conda and texlive, for standardising environments across the MalariaGEN resource centre team.
License: MIT License
Hot on the heels of 2.7.0, version 2.8.0 of dask and distributed has come out. I can't see anything critical in there so I don't think it's urgent to upgrade now, but just noting these are available.
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Despite the pinned environment solving previously, CI builds are failing for vector-ops PRs, e.g. https://travis-ci.com/github/malariagen/vector-ops/builds/177765974
I'll try recreating the pinned environment files.
I'd like to add xpclr to binder, but when I install directly from conda, it wants to downgrade all blas
The following packages will be downloaded:
package | build
---------------------------|-----------------
gsl-2.2.1 | h0c605f7_3 2.6 MB
libgfortran-ng-7.2.0 | hdf63c60_3 1.2 MB conda-forge
mkl_random-1.0.2 | py36_0 1.3 MB conda-forge
numpy-1.13.3 | py36hdbf6ddf_4 3.9 MB
scikit-learn-0.19.1 | py36hedc7406_0 5.2 MB
mkl_fft-1.0.10 | py36_0 650 KB conda-forge
scipy-1.0.1 | py36hfc37229_0 17.8 MB
mkl-2018.0.3 | 1 198.7 MB
blas-1.0 | mkl 6 KB
xpclr-1.1 | py_0 14 KB bioconda
intel-openmp-2019.1 | 144 885 KB
------------------------------------------------------------
Total: 232.3 MB
The following NEW packages will be INSTALLED:
intel-openmp: 2019.1-144
libgfortran-ng: 7.2.0-hdf63c60_3 conda-forge
mkl: 2018.0.3-1
mkl_fft: 1.0.10-py36_0 conda-forge
mkl_random: 1.0.2-py36_0 conda-forge
xpclr: 1.1-py_0 bioconda
The following packages will be DOWNGRADED:
blas: 1.1-openblas conda-forge --> 1.0-mkl
gsl: 2.2.1-blas_openblash47a8a8e_5 conda-forge [blas_openblas] --> 2.2.1-h0c605f7_3
numpy: 1.13.3-py36_blas_openblas_201 conda-forge [blas_openblas] --> 1.13.3-py36hdbf6ddf_4
scikit-learn: 0.19.1-py36_blas_openblas_201 conda-forge [blas_openblas] --> 0.19.1-py36hedc7406_0
scipy: 1.0.1-py36_blas_openblas_200 conda-forge [blas_openblas] --> 1.0.1-py36hfc37229_0
I've just verified that if I add xpclr to the binder env.yml, the numpy install is py36hdbf6ddf_4 not 1.13.3-py36_blas_openblas_201 I'm not sure if this is a channel ordering issue?
Doing v4.2.1 installation I encountered an error
conda.exceptions.ResolvePackageNotFound:
- owslib==0.19.0=py_1
It seems to happen because this package is labelled broken in conda-forge
Solution that worked for me: replace an entry in pinned environment to
- owslib=0.19.0=py_2
The script install-conda.sh doesn't work on Mac, where wget is not installed by default. The offending line is:
wget --no-clobber https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.shwget should be replaced with macOX-native curl. The following should have equivalent behaviour:
curl -C - -O https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.shAfter creating an environment using binder as a submodule, I'm finding I can't import pysamstats:
$ python
Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 02:32:25)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysamstats
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/nfs/team112_internal/rp7/src/github/malariagen/Pf-6.0-public-release/deps/conda/envs/Pf-6.0-public-release/lib/python3.6/site-packages/pysamstats/__init__.py", line 8, in <module>
from .pileup import *
File "/nfs/team112_internal/rp7/src/github/malariagen/Pf-6.0-public-release/deps/conda/envs/Pf-6.0-public-release/lib/python3.6/site-packages/pysamstats/pileup.py", line 6, in <module>
import pysamstats.opt as opt
File "libcfaidx.pxd", line 52, in init pysamstats.opt
AttributeError: module 'pysam.libcfaidx' has no attribute 'FastxRecord'
@alimanfoo any suggestions?
Heatmap plotting is broken when using combination
seaborn=0.9.0
matplotlib=3.1.1
This is a documented problem mwaskom/seaborn#1773. My solution was to downgrade matplotlib to matplotlib=3.1.0. The bug should be also fixed in matplotlib=3.1.2, which is currently not released.
Hi, can we include snakemake>=5.10.0 in the next binder release?
It introduces integration with jupyter notebooks, which basically means no need to convert code into plain python scripts after development in jupyter. I wanted to play around with this feature, but was carried away by other projects. Thus, leaving a reminder here.
Hi @alimanfoo
Frequent use case of binder update is its application to non-master working branch. I believe you posted commands on how to do it, but I lost track of those. Maybe you could add this list of commands to binder readme?
I have created a docker image based on binder release v2.4.2 and deployed it to
our dev cluster https://testlab.malariagen.net
I'm getting a 500 server error when I open the dask status page as well as the following errors while running the sample notebook
bokeh.util.tornado - ERROR - Error thrown from periodic callback:
bokeh.util.tornado - ERROR - Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/opt/conda/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/opt/conda/lib/python3.7/site-packages/bokeh/server/session.py", line 70, in _needs_document_lock_wrapper
result = yield yield_for_all_futures(func(self, *args, **kwargs))
File "/opt/conda/lib/python3.7/site-packages/bokeh/server/session.py", line 191, in with_document_locked
return func(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/bokeh/document/document.py", line 1127, in wrapper
return doc._with_self_as_curdoc(invoke)
File "/opt/conda/lib/python3.7/site-packages/bokeh/document/document.py", line 1113, in _with_self_as_curdoc
return f()
File "/opt/conda/lib/python3.7/site-packages/bokeh/document/document.py", line 1126, in invoke
return f(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/distributed/dashboard/components/init.py", line 78, in
doc.add_periodic_callback(lambda: update(ref), interval)
File "/opt/conda/lib/python3.7/site-packages/distributed/dashboard/components/init.py", line 85, in update
comp.update()
File "/opt/conda/lib/python3.7/site-packages/bokeh/core/property/validation.py", line 97, in func
return input_function(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/distributed/dashboard/components/scheduler.py", line 1435, in update
d = progress_quads(state)
File "/opt/conda/lib/python3.7/site-packages/distributed/diagnostics/progress_stream.py", line 105, in progress_quads
rl = width * r / a + l
ZeroDivisionError: float division by zero
Hi @alimanfoo,
It seems that binder update requires a number of follow-up actions in the dependent repos: update within each repo, environment updates for multiple repo users, sometimes in multiple instances. Maybe we should post certain version of binder as a release to notify everyone that it is time to get an updated version installed?
The nb_conda_kernels package dynamically scans the local system for all available conda environments. This can produce a long list of environments, and is more confusing than useful. I.e., we never want to launch jupyter notebook/lab with one environment then open a notebook using a different kernel. Let's remove it.
A new release of intake should be imminent, including a new feature to make data catalogs including zarr data sources. When release is available, upgrade binder.
Looking through conda docs, it seems that the recommended way of creating the identical environment is creation of spec files with
conda list --explicit > spec-file.txt
Which then can be used instead of yml
conda create --name myenv --file spec-file.txt
I wonder if we could/should use those spec files instead of pinned environments as linux/MacOs specific snapshots. Or am I missing some point here?
I was a bit unclear about exactly how I should use this repo before talking through with Alistair, so thought it might be useful to try to update the README for users such as me, giving a bit more explanation of the situations in which each set of commands needs to be run.
Add the adlfs package which allows reading and writing to Azure blob storage.
Ref. https://github.com/malariagen/vector-ops/pull/1139
Non-critical glitch using Zarr tree() in MalariaGEN Datalab notebooks. The tree actually outputs/prints OK, but complains No module named 'ipytree'. Maybe something missing somewhere? Screenshots of the error below.
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj)
916 method = get_real_method(obj, self.print_method)
917 if method is not None:
--> 918 method()
919 return True
920
/opt/conda/lib/python3.7/site-packages/zarr/util.py in _ipython_display_(self)
492
493 def _ipython_display_(self):
--> 494 tree = tree_widget(self.group, expand=self.expand, level=self.level)
495 tree._ipython_display_()
496 return tree
/opt/conda/lib/python3.7/site-packages/zarr/util.py in tree_widget(group, expand, level)
429
430 def tree_widget(group, expand, level):
--> 431 import ipytree
432
433 result = ipytree.Tree()
ModuleNotFoundError: No module named 'ipytree'
bcolz 1.2.1 should be available via conda-forge soon. Not a high priority but would be good to upgrade.
Just realized I was using a newer version of snakemake for my workflows. The newest version is
snakemake=5.3.1, which seemingly has CWL export option. But feature that I used (directory output type) was added in snakemake=5.2.0. Can we update the environment.yml:L51 to either of those?
As a side-effect it might be needed to introduce a couple of changes in the pipelines, as the directory usage is not backwards compatible, i.e. mandatory in newer versions and cannot be used in older versions.
Here's the line: https://github.com/malariagen/binder/blob/7c0086d14bbdf6d0e3bbf18f55cc2df1e8801238/environment.yml#L51
Non-urgent but a reminder for the next iteration of binder
This will ensure that if you install environment from a local clone of binder, the deps directory will not be tracked in github
In Mac OS, error occurs when running pypi installation of pysam
htslib/cram/cram_io.c:63:10: fatal error: 'os/lzma_stub.h' file not found
#include "os/lzma_stub.h"
^~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
Issue in pysam pysam-developers/pysam#645 does not give much options apart from using pysam 0.13.
Is it possible that the same error causes installation of pysam 0.13 instead of 0.15.1 via conda? (this is how I understand the reason we use pypi instead of conda for pysam installation)
Related to #10
Currently sourcing of env.sh works only from directory which holds binder (e.g., vector-ops). I would like to be able to source it from any dir.
This can be done by replacing
$(pwd)
with something like
repoDir=$(cd `dirname $0/../` && pwd)
I suspect that more elegant solution exists for this, so not making a PR.
Add a test to travis CI that all packages can be imported. Should catch problems like #10.
pyprojroot looks like a useful package.
On a fresh ubuntu install (18.04.4 LTS), binder install fails due to lack of gcc.
Installing gcc fixed the problem, but it might be good to add this requirement to the documentation.
I have recently used R kernel for Jupyter (https://github.com/IRkernel/IRkernel) which was straightforward to install and allows you to run R in jupyter notebooks just like you would use python. I intend to create a PR when I next need to use R. In the meantime, please shout if you have strong objections to this.
One thing I did realise when doing this is that R packages should be installed using conda, rather than R's own install.packages or other methods. See https://docs.anaconda.com/anaconda/packages/r-language-pkg-docs/. E.g. to install ape use conda install -c r r-ape.
Steps to reproduce:
Having existing binder installation on Mac OS, do
./binder/install-conda.sh
source binder/env.sh
python
>>> import numpy
Result:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
from . import core
File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/core/__init__.py", line 67, in <module>
raise ImportError(msg.format(path))
ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version.
Now trying to reinstall binder from scratch by removing binder/deps
UPD binder reinstall from scratch solved this problem
@alimanfoo commented on Sun May 13 2018
Pyfaidx is apparently the new thing. Need version 0.5.4 or later for numpy array support.
Having problems installing the environment on the cluster.
sean@india:~/vector-ops$ ./binder/install-conda.sh
[binder] skipping miniconda installation
[binder] installing packages
[binder] install conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.7.11
latest version: 4.7.12
Please update conda by running
$ conda update -n base conda
# All requested packages already installed.
conda 4.7.11
[binder] check channel priority - this must be 'true' or 'flexible', ***not*** 'strict'
channel_priority: flexible
[binder] creating environment vector-ops-3d37be2 from /home/sean/vector-ops/binder/environment-pinned-linux.yml
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Traceback (most recent call last):
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
return func(*args, **kwargs)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 73, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 101, in execute
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 27, in install
unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 116, in solve_for_transaction
should_retry_solve)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 157, in solve_for_diff
force_remove, should_retry_solve)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 274, in solve_final_state
ssc = self._add_specs(ssc)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 554, in _add_specs
explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 520, in _get_package_pool
pool = self.get_reduced_index(specs)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 541, in get_reduced_index
explicit_specs, features = self.verify_specs(explicit_specs)
File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 280, in verify_specs
raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound:
- ipython==7.9.0=py36h5ca1d4c_0
sean@india:~/vector-ops$
Path is
sean@india:~/vector-ops$ echo @$PATH
@/home/sean/bin:/home/sean/.local/bin:/home/sean/bin:/home/sean/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/puppetlabs/bin
sean@india:~/vector-ops$
Causing build failures
Downloading and Extracting Packages
certifi-2019.9.11 | 147 KB | ##################################### | 100%
conda-4.7.11 | 3.0 MB | ##################################### | 100%
ca-certificates-2019 | 144 KB | ##################################### | 100%
openssl-1.1.1d | 2.1 MB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
conda 4.7.11
[binder] check channel priority - this must be 'true' or 'flexible', ***not*** 'strict'
channel_priority: flexible
[binder] creating environment vector-ops-3d37be2 from /home/travis/build/malariagen/vector-ops/binder/environment-pinned-linux.yml
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Traceback (most recent call last):
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
return func(*args, **kwargs)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 73, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 101, in execute
installer.install(prefix, pkg_specs, args, env)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 27, in install
unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 116, in solve_for_transaction
should_retry_solve)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 157, in solve_for_diff
force_remove, should_retry_solve)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 274, in solve_final_state
ssc = self._add_specs(ssc)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 554, in _add_specs
explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 520, in _get_package_pool
pool = self.get_reduced_index(specs)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 541, in get_reduced_index
explicit_specs, features = self.verify_specs(explicit_specs)
File "/home/travis/build/malariagen/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 280, in verify_specs
raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound:
- ipython==7.9.0=py36h5ca1d4c_0
The command "./binder/install-conda.sh" failed and exited with 1 during .
Your build has been stopped.
Listed as broken in Conda
https://anaconda.org/conda-forge/ipython/files?version=7.9.0
https://anaconda.org/conda-forge/repo/files?type=any&label=broken
Currently the main linux environment file is called "environment-pinned-linux.yml". This is nice and descriptive, however it means that this module can no longer be used as a submodule to create mybinder-launchable repos, because mybinder expects a file called "environment.yml".
Proposed to change the name of "environment-pinned-linux.yml" to "environment.yml". For simplicity, proposed to also rename "environment-pinned-osx.yml" to "environment-osx.yml".
Don't know how easy, but would be cool to add in MacOS CI to check everything installs on all platforms.
should be Miniconda3-latest-MacOSX-x86_64.sh
Hi @alimanfoo @hardingnj. Our current dependencies installation method seemingly does not handle conda updates, so when running binder/install-conda.sh I get
==> WARNING: A newer version of conda exists. <==
current version: 4.5.12
latest version: 4.6.4
Should we include conda update in this script?
The latest travis CI build (see #29 and https://travis-ci.org/malariagen/binder/jobs/483115513) failed on linux as msprime could not be imported.
Add support for windows users, at least for installing conda and creating the conda environment. Should be possible for most packages, although I believe the bioconda packages won't be available for windows. Work would be to create a windows batch file or similar which is equivalent to the install-conda.sh script.
Says:
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
Needed for the VGSC report.
I got the following errors while running install-conda.sh on a mac
$ ./binder/install-conda.sh
bash: Miniconda3-latest-MaxOSX-x86_64.sh: No such file or directory
One hacky way to resolve this is by modifying the script:
if [ "$(uname)" == "Darwin" ]; then
....
chmod ug+x Miniconda3-latest-MacOSX-x86_64.sh
# install miniconda
./Miniconda3-latest-MacOSX-x86_64.sh -b -p ../$CONDADIR
Here's how I test binder updates in the independent repo. Tricky points here are to deactivate any envs and to do cd .. prior to conda installation to avoid an ambiguous error SpecNotFound: Invalid name, try the format: user/package.
Maybe this procedure can be improved and then documented in the readme?
Clone the repo, create new branch
git clone [email protected]:malariagen/binder.git
cd binder
git checkout -b issue_name
git push --set-upstream origin issue_name
# make some changes
Test if it did not break the installation process, but first make sure that no environment is activated, otherwise run source deactivate. Then do
cd ..
./binder/install_conda.sh
source ./binder/env.sh
# check package versions and resolve version conflicts
If all went well, push changes
cd binder
git add environment.yml
git commit -m '###'
git push
# do PR
Optional clean-up
rm -r ../deps
This behaviour may affect other venvs on the system: there might be no alternative, but might be worth thinking about this behaviour?
re: https://github.com/malariagen/vector-ops/issues/701#issuecomment-516829196
cc @EricRLucas
In MacOS, samtools cannot be run due to an error:
$ samtools
dyld: Symbol not found: _stdscr
Referenced from: /Users/am60/malaria/malariagen/binder/conda/envs/vector-ops/bin/samtools
Expected in: /Users/am60/malaria/malariagen/binder/conda/envs/vector-ops/bin/../lib/libncursesw.6.dylib
in /Users/am60/malaria/malariagen/binder/conda/envs/vector-ops/bin/samtools
Abort trap: 6
After some googling it seems that this can be fixed by installing ncurses from conda forge by adding
- conda-forge::ncurses to environment.yml
The install-conda.sh script is failing for me [version c668a73], reporting:
conda.exceptions.ResolvePackageNotFound:
- pandas==0.25.0=py36hb3f55d8_0
which appears to be set in environment-pinned-linux.yml.
Have I forgotten a step?
This is just a thought, but I wonder if it would be a good idea if the install-conda.sh script includes either the git tag (or the commit hash if using an untagged commit) in the name of the conda environment being created. E.g., if running from within vector-ops, would create an environment named "vector-ops-binder-v1.2.1" if using v1.2.1 of binder, or "vector-ops-binder-e4a69fcd" if using binder commit e4a69fc. This would allow some transparency of what the current state of the conda environment is. Also, when rerunning install-conda.sh after a binder upgrade, it would create a new environment alongside the previous environment. That way it is possible to switch between environments if needed.
@alimanfoo mentioned that might be worthwhile
Simply running
conda install -c conda-forge umap-learn
from within binder env results in a bunch of version conflicts. Is there a better way around it?
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