diff options
| -rw-r--r-- | README.md | 21 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 2 | ||||
| -rw-r--r-- | doc/INSTALL.md | 31 |
3 files changed, 37 insertions, 17 deletions
@@ -122,19 +122,7 @@ It should print some instructions about how to use the uploader. ## Installation with GNU Guix -Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. - -1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: - -```sh -~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs -``` - -2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: - -```sh -pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master -``` +For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL.md) # Usage @@ -148,7 +136,7 @@ bh20-seq-uploader example/sequence.fasta example/metadata.json All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself. -Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run: +An example is to get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run a series of commands ```sh minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf @@ -157,6 +145,7 @@ odgi build -g seqs.gfa -s -o seqs.odgi odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5 ``` -For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). - +Here we convert such a pipeline into the Common Workflow Language (CWL) and +sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate). +For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 56cbe22..bf74ea5 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -6,7 +6,7 @@ import json import urllib.request import socket import getpass -from .qc_metadata import qc_metadata +import qc_metadata ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' diff --git a/doc/INSTALL.md b/doc/INSTALL.md new file mode 100644 index 0000000..c5c486c --- /dev/null +++ b/doc/INSTALL.md @@ -0,0 +1,31 @@ +# INSTALLATION + +Other options for running this tool. + +## GNU Guix + +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. + +1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: + +```sh +~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +``` + +2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: + +```sh +pip3 install --user schema-salad arvados-python-client +``` + +Pip installed the following modules + +``` +arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1 +``` + +3. Run the tool directly with + +```sh +~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py +``` |