gusef
commented
7 years ago Is your hydra environment still activated? Make sure it is not. And when I built it this morning I used the conda version that you get when you 'module load anaconda2'
Closed ericreed closed 7 years ago
gusef
commented
7 years ago Is your hydra environment still activated? Make sure it is not. And when I built it this morning I used the conda version that you get when you 'module load anaconda2'
ericreed
commented
7 years ago No the environment is not activated. I tried again using anaconda2. Now I'm getting a different error (below),
Solving package specifications: . Error: Packages/dependencies missing in current linux-64 channels:
gusef
commented
7 years ago Just installed it, worked without any issues. Here are the exact lines of code I used:
qrsh -P montilab-p
module load anaconda2
cd /restricted/projectnb/montilab-p/projects/pipeline_dev/Hydra/conda_packages
WORKSPACE=/restricted/projectnb/montilab-p/projects/pipeline_dev
export CONDA_BLD_PATH=$WORKSPACE/conda_build_space
conda build hydra-1.0.0
Since we use the same conda version and hydra is installed from the github repo it is probably your recipe?
The only thing that I haven't gotten to work yet is setting the standard anaconda_env, which currently points to the home directory. This is where the additional packages are downloaded. Let me know if you find a fix for that. Tired of deleting that directory every single time I rebuild.
gusef
commented
7 years ago Hey Eric, did you resolve this issue? Can you please close open issues once they are resolved?
I'm trying to build the conda package using the conda package guide and keep getting an error. Right now I'm just trying to run conda build hydra-1.0.0 using the original git source (no changes). I'm running the code in the help page (subbing in my own directories of course). I've printed the output below, the final line has the error. Any help it welcome.
Removing old build directory Removing old work directory BUILD START: hydra-1.0.0-monti_2 Fetching package metadata: ........
WARNING: conda-build appears to be out of date. You have version 1.11.0 but the latest version is 2.0.7. Run
conda update -n root conda-build
to get the latest version.
Solving package specifications: ....................... The following NEW packages will be INSTALLED:
Linking packages ... [ COMPLETE ] |##################################################################################################################| 100% dbus post-link :: /etc/machine-id not found .. dbus post-link :: .. using /proc/sys/kernel/random/boot_id Removing old work directory Password: checkout: u'v1.0.0' Initialized empty Git repository in /restricted/projectnb/montilab-p/personal/eric/condaWS/conda_build_space/work/.git/ Note: checking out 'v1.0.0'.
You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:
git checkout -b new_branch_name
HEAD is now at 1041d98... Changed version number of Hydra ==> git log -n1 <==
commit 1041d98440c8056747de549064fc1e643768de80 Author: montilab montilab@bu.edu Date: Tue Jun 16 14:52:02 2015 -0400
==> git describe --tags --dirty <==
v1.0.0
==> git status <==
Not currently on any branch.
nothing to commit (working directory clean)
Package: hydra-1.0.0-monti_2 source tree in: /restricted/projectnb/montilab-p/personal/eric/condaWS/conda_build_space/work
Installed /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages/hydra-2.0.0-py2.7.egg Processing dependencies for hydra==2.0.0 Searching for biopython==1.65 Best match: biopython 1.65 Adding biopython 1.65 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for pysam==0.6 Best match: pysam 0.6 Adding pysam 0.6 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for matplotlib==1.4.3 Best match: matplotlib 1.4.3 Adding matplotlib 1.4.3 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for numpy==1.9.3 Best match: numpy 1.9.3 Adding numpy 1.9.3 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for mock==2.0.0 Best match: mock 2.0.0 Adding mock 2.0.0 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for nose==1.3.7 Best match: nose 1.3.7 Adding nose 1.3.7 to easy-install.pth file Installing nosetests script to /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/bin Installing nosetests-2.7 script to /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/bin
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for pyparsing==2.0.3 Best match: pyparsing 2.0.3 Adding pyparsing 2.0.3 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for pytz==2016.7 Best match: pytz 2016.7 Adding pytz 2016.7 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for python-dateutil==2.5.3 Best match: python-dateutil 2.5.3 Adding python-dateutil 2.5.3 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for six==1.10.0 Best match: six 1.10.0 Adding six 1.10.0 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for funcsigs==1.0.2 Best match: funcsigs 1.0.2 Adding funcsigs 1.0.2 to easy-install.pth file
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Searching for pbr==1.10.0 Best match: pbr 1.10.0 Adding pbr 1.10.0 to easy-install.pth file Installing pbr script to /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/bin
Using /usr3/graduate/reeder/.conda/envs/_build_placehold_placehold_placehold_placehold/lib/python2.7/site-packages Finished processing dependencies for hydra==2.0.0 compiling .pyc files... number of files: 66 Detected hard-coded path in text file bin/hydra-rnaseq Detected hard-coded path in text file bin/nosetests-2.7 Detected hard-coded path in text file bin/paired_ends_intersect.py Detected hard-coded path in text file bin/run_bamqc Detected hard-coded path in text file bin/run_bamqc.py Detected hard-coded path in text file bin/run_cufflinks Detected hard-coded path in text file bin/run_cutadapt Detected hard-coded path in text file bin/run_fastqc Detected hard-coded path in text file bin/run_featureCount Detected hard-coded path in text file bin/run_htseq Detected hard-coded path in text file bin/run_matched_pairs Detected hard-coded path in text file bin/run_star Detected hard-coded path in text file bin/run_tophat Detected hard-coded path in text file lib/python2.7/site-packages/hydra-2.0.0-py2.7.egg/EGG-INFO/scripts/paired_ends_intersect.py BUILD END: hydra-1.0.0-monti_2 TEST START: hydra-1.0.0-monti_2 Fetching package metadata: ........
WARNING: conda-build appears to be out of date. You have version 1.11.0 but the latest version is 2.0.7. Run
conda update -n root conda-build
to get the latest version.
Solving package specifications: Error: Could not find some dependencies for hydra 1.0.0 monti_2: bowtie2 2.2.2