Steve
2018-03-27 20:29:04 UTC
I am trying to make a conda env from the source located here:
http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
the contents of which look like this:
$ ls -1 annovar/
annotate_variation.pl
coding_change.pl
convert2annovar.pl
example
humandb
retrieve_seq_from_fasta.pl
table_annovar.pl
variants_reduction.pl
so, in my conda env, I ultimately need to end up with a dir that contains
these files, and it needs to be pre-pended to my $PATH when I activate the
env.
To build a local conda package out of this, I set up my local directory
like this:
$ tree annovar-150617/
annovar-150617/
|-- build.sh
|-- environment.yml
`-- meta.yaml
and the files look like this:
$ cat annovar-150617/build.sh
#!/bin/bash
set -x -e
wget http:
//www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
tar xvfz annovar.revision150617.tar.gz
rm -f annovar.revision150617.tar.gz
$ cat annovar-150617/meta.yaml
package:
name: annovar
version: "150617"
source:
url: http:
//www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
build:
script: build.sh
noarch: generic
outputs:
- name: annovar
version: "150617"
files:
- annovar
$ cat annovar-150617/environment.yml
name: annovar-150617
and I build and install the package with the following command:
source "/shared/miniconda3/bin/activate" && \
package_path="$(conda-build annovar-150617 --output --no-force-upload
--no-anaconda-upload)" && \
echo "$package_path" && \
conda install --use-local "$package_path" -n annovar-150617
output:
/home/kellys04/conda-bld/noarch/annovar-150617-0.tar.bz2
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
When I check that the package is installed in the conda env specified, I
get the following output:
source "/shared/miniconda3/bin/activate" annovar-150617 && \
conda list && \
echo ${PATH} && \
echo ${PYTHONPATH}
# packages in environment at /home/kellys04/.conda/envs/annovar-150617:
#
# Name Version Build Channel
annovar 150617 0 local
/home/kellys04/.conda/envs/annovar-150617/bin:/opt/oss-mldl/bin:/opt/at10.0/
bin:/opt/ibm/lsfsuite/lsf/10.1/linux3.10-glibc2.17-ppc64le/etc:/opt/ibm/
lsfsuite/lsf/10.1/linux3.10-glibc2.17-ppc64le/bin:/usr/local/bin:/usr/bin:
/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/kellys04/.local/bin:/home/
kellys04/bin
However, there is a problem here: the path that has been pre-pended to my
$PATH does not actually exist:
$ ll /home/kellys04/.conda/envs/annovar-150617/bin
ls: cannot access /home/kellys04/.conda/envs/annovar-150617/bin: No such
file or directory
The only thing that has been output there is this 'conda-meta' directory:
$ ls -1 /home/kellys04/.conda/envs/annovar-150617/conda-meta/
annovar-150617-0.json
history
And if I activate the env, the scripts from the source package are not
loaded:
$ source "/shared/miniconda3/bin/activate" annovar-150617 &&
annotate_variation.pl --version
-bash: annotate_variation.pl: command not found
Any ideas? What did I miss?
http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
the contents of which look like this:
$ ls -1 annovar/
annotate_variation.pl
coding_change.pl
convert2annovar.pl
example
humandb
retrieve_seq_from_fasta.pl
table_annovar.pl
variants_reduction.pl
so, in my conda env, I ultimately need to end up with a dir that contains
these files, and it needs to be pre-pended to my $PATH when I activate the
env.
To build a local conda package out of this, I set up my local directory
like this:
$ tree annovar-150617/
annovar-150617/
|-- build.sh
|-- environment.yml
`-- meta.yaml
and the files look like this:
$ cat annovar-150617/build.sh
#!/bin/bash
set -x -e
wget http:
//www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
tar xvfz annovar.revision150617.tar.gz
rm -f annovar.revision150617.tar.gz
$ cat annovar-150617/meta.yaml
package:
name: annovar
version: "150617"
source:
url: http:
//www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.revision150617.tar.gz
build:
script: build.sh
noarch: generic
outputs:
- name: annovar
version: "150617"
files:
- annovar
$ cat annovar-150617/environment.yml
name: annovar-150617
and I build and install the package with the following command:
source "/shared/miniconda3/bin/activate" && \
package_path="$(conda-build annovar-150617 --output --no-force-upload
--no-anaconda-upload)" && \
echo "$package_path" && \
conda install --use-local "$package_path" -n annovar-150617
output:
/home/kellys04/conda-bld/noarch/annovar-150617-0.tar.bz2
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
When I check that the package is installed in the conda env specified, I
get the following output:
source "/shared/miniconda3/bin/activate" annovar-150617 && \
conda list && \
echo ${PATH} && \
echo ${PYTHONPATH}
# packages in environment at /home/kellys04/.conda/envs/annovar-150617:
#
# Name Version Build Channel
annovar 150617 0 local
/home/kellys04/.conda/envs/annovar-150617/bin:/opt/oss-mldl/bin:/opt/at10.0/
bin:/opt/ibm/lsfsuite/lsf/10.1/linux3.10-glibc2.17-ppc64le/etc:/opt/ibm/
lsfsuite/lsf/10.1/linux3.10-glibc2.17-ppc64le/bin:/usr/local/bin:/usr/bin:
/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/kellys04/.local/bin:/home/
kellys04/bin
However, there is a problem here: the path that has been pre-pended to my
$PATH does not actually exist:
$ ll /home/kellys04/.conda/envs/annovar-150617/bin
ls: cannot access /home/kellys04/.conda/envs/annovar-150617/bin: No such
file or directory
The only thing that has been output there is this 'conda-meta' directory:
$ ls -1 /home/kellys04/.conda/envs/annovar-150617/conda-meta/
annovar-150617-0.json
history
And if I activate the env, the scripts from the source package are not
loaded:
$ source "/shared/miniconda3/bin/activate" annovar-150617 &&
annotate_variation.pl --version
-bash: annotate_variation.pl: command not found
Any ideas? What did I miss?
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