Hi,
Not sure if I should put this here, or on conda, but Ill try you first and maybe cross post there.
I’m having issues getting qiime2 running on a local server. Ive got an interesting set up. To limit the number of copies of QIIME 2 floating around, Im trying to set up a single folder with the programs to demonstrate critical mass. However, due to permissions issues, this has resulted in at least three conda installations: my homedir, and two folders with specific permissions.
Ive sucessfully gotten qiime2-2018.11 and qiime2-2019.1 running in the two older conda enviroments. But, I just installed conda 4.5.12 and then tried to run the QIIME installation for both qiime2-2018.11 and qiime2-2019.1, they failed.
After downloading mini conda and running the installation package set up and directing it to a unique directory. Then, I updated conda and got wget.
conda update conda
conda install wget
The both work fine, and I get nice feedback from the wget installation:
Solving environment: done
## Package Plan ##
environment location: /nfs/projects/qiime2/miniconda3
added / updated specs:
- wget
The following packages will be downloaded:
package | build
---------------------------|-----------------
wget-1.19.5 | h20c2e04_0 750 KB
The following NEW packages will be INSTALLED:
wget: 1.19.5-h20c2e04_0
Then, I went to install qiime2 per the instructions:
wget https://data.qiime2.org/distro/core/qiime2-2019.1-py36-linux-conda.yml
conda env create -n qiime2-2019.1 --file qiime2-2019.1-py36-linux-conda.yml
And, now, Im getting the following error message:
Solving environment: failed
ResolvePackageNotFound:
- perl-carp=1.38
- dbus=1.13.0
- mkl_fft=1.0.10
- pillow=5.4.1
- jpeg=9c
- gtk2=2.24.31
- q2-longitudinal=2019.1.0
- sortmerna=2.0
- r-data.table=1.11.4
- pandoc=2.5
- q2-emperor=2019.1.0
- xorg-xproto=7.0.31
- r-lambda.r=1.2.3
- r-base[version='>=3.5.1,<3.5.2.0a0']
- fontconfig=2.13.1
- qiime2=2019.1.0
- tbb=2019.3
- perl-compress-raw-bzip2=2.084
- entrypoints=0.3
- q2-alignment=2019.1.0
- deblur=1.1.0
- q2-diversity=2019.1.0
- r-pillar=1.3.0
- r-base[version='>=3.5.1,<3.5.2.0a0']
- r-pillar=1.3.0
- r-fansi
- h5py=2.9.0
- q2-metadata=2019.1.0
- q2-composition=2019.1.0
- q2-quality-filter=2019.1.0
- q2templates=2019.1.0
- bokeh=1.0.4
- r-hwriter=1.3.2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- xorg-libsm=1.2.3
- q2-quality-control=2019.1.0
- xorg-renderproto=0.11.1
- graphite2=1.3.13
- libtiff=4.0.10
- r-rcurl=1.95_4.11
- scipy=1.2.0
- bioconductor-s4vectors=0.16.0
- gneiss=0.4.4
- biom-format
- bioconductor-biocgenerics=0.24.0
- perl-list-moreutils=0.428
- q2-vsearch=2019.1.0
- perl-test-more=1.001002
- fastcluster=1.1.25
- scikit-learn=0.20.2
- q2-fragment-insertion=2019.1.0
- q2-dada2=2019.1.0
- raxml=8.2.12
- fasttree=2.1.10
- perl-list-moreutils-xs=0.428
- r-scales=1.0.0
- xorg-libxau=1.0.8
- pytest=4.1.1
- q2-gneiss=2019.1.0
- gdk-pixbuf=2.36.12
- openjdk=11.0.1
- xorg-libx11=1.6.6
- perl-compress-raw-zlib=2.084
- emperor=1.0.0beta18
- xorg-libxt=1.1.5
- atk=2.25.90
- perl-xsloader=0.24
- bioconductor-zlibbioc=1.24.0
- tk=8.6.9
- bioconductor-rsamtools=1.30.0
- matplotlib-base=3.0.2
- pip=19.0.1
- bioconductor-biocparallel=1.12.0
- xorg-xextproto=7.3.0
- bioconductor-iranges=2.12.0
- bioconductor-xvector=0.18.0
- q2-feature-table=2019.1.0
- r-mass=7.3_50
- mafft=7.310
- r-matrixstats=0.54.0
- pigz=2.3.4
- krb5=1.14.6
- blast=2.7.1
- r-snow=0.4_3
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bioconductor-genomeinfodb=1.14.0
- q2-deblur=2019.1.0
- r-digest=0.6.18
- pango=1.40.14
- gnutls=3.5.19
- perl-exporter=5.72
- setuptools=40.7.1
- pyrsistent=0.14.9
- bioconductor-genomicalignments=1.14.1
- msgpack-python=0.6.1
- r-permute=0.9_4
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bioconductor-genomeinfodbdata=1.0.0
- biom-format=2.1.7
- bioconductor-delayedarray=0.4.1
- r-futile.logger=1.4.3
- r-base[version='>=3.5.1,<3.5.2.0a0']
- r-futile.logger=1.4.3
- r-futile.options
- r-futile.logger=1.4.3
- r-lambda.r[version='>=1.1.0']
- q2cli=2019.1.0
- xorg-libice=1.0.9
- cutadapt=1.18
- q2-feature-classifier=2019.1.0
- xorg-kbproto=1.0.7
- perl-archive-tar=2.32
- q2-phylogeny=2019.1.0
- xorg-libxdmcp=1.1.2
- r-rlang=0.3.0.1
- bioconductor-biostrings=2.46.0
- perl-extutils-makemaker=7.34
- scikit-bio=0.5.5
- ca-certificates=2018.11.29
- r-utf8=1.1.4
- libarbdb=6.0.6
- arb-bio-tools=6.0.6
- q2-cutadapt=2019.1.0
- q2-demux=2019.1.0
- r-ggplot2=3.1.0
- r-base[version='>=3.5.1,<3.5.2.0a0']
- r-ggplot2=3.1.0
- r-rlang[version='>=0.2.1']
- q2-taxa=2019.1.0
- r-munsell=0.5.0
- r-base[version='>=3.5.1,<3.5.2.0a0']
- r-rcppparallel=4.4.1
- xorg-libxrender=0.9.10
- bioconductor-genomicranges=1.30.3
- nettle=3.3
- r-mgcv=1.8_24
- r-stringr=1.3.1
- r-base[version='>=3.5.1,<3.5.2.0a0']
- perl-scalar-list-utils=1.45
- iqtree=1.6.9
- bioconductor-dada2=1.6.0
- unifrac=0.9.3
- jsonschema=3.0.0a3
- r-stringi=1.2.4
- bioconductor-shortread=1.36.0
- bioconductor-biobase=2.38.0
- perl-io-zlib=1.10
- r-rcpp=1.0.0
- gstreamer=1.12.5
- r-glue=1.3.0
- vsearch=2.7.0
- perl-io-compress=2.084
- perl-pathtools=3.73
- libpng=1.6.36
- pthread-stubs=0.4
- r-futile.options=1.0.1
- r-base[version='>=3.5.1,<3.5.2.0a0']
- r-vegan=2.5_3
- libuuid=2.32.1
- sina=1.4.0
- q2-types=2019.1.0
- harfbuzz=1.9.0
- bioconductor-summarizedexperiment=1.8.0
- xorg-libxext=1.3.3
- q2-sample-classifier=2019.1.0
- perl-exporter-tiny=1.002001
- r-fansi=0.3.0
I tried just installing scipy, pandas, and numpy in a test python 3.6.7 enviroment.
conda create --name base_test python=3.6.7 numpy scipy pandas matplotlib jupyter
This ran just fine, and quick test with ipython shows everything imports correctly.