diff --git a/docs/README.md b/docs/README.md index f44e791..e311beb 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io) +# -# geofetch +[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io) `geofetch` is a command-line tool that does two things when given one or more GEO/SRA accessions: diff --git a/docs/faq.md b/docs/faq.md new file mode 100644 index 0000000..de63b57 --- /dev/null +++ b/docs/faq.md @@ -0,0 +1,13 @@ +# FAQ + + +## I get an error: `geofetch: command not found` after installing. Why isn't the `geofetch` executable in my path? + + +By default, Python packages are installed to `~/.local/bin`. You can add this location to your path by appending it: + +``` +export PATH=$PATH:~/.local/bin +``` + +Add this line to your `.bashrc` or `.profile` to make it permanent. diff --git a/docs/img/geofetch_logo_dark.svg b/docs/img/geofetch_logo_dark.svg index 62476bf..ed90258 100644 --- a/docs/img/geofetch_logo_dark.svg +++ b/docs/img/geofetch_logo_dark.svg @@ -15,7 +15,7 @@ id="svg4818" version="1.1" inkscape:version="0.91 r13725" - sodipodi:docname="geofetch_logo.svg"> + sodipodi:docname="geofetch_logo_dark.svg"> @@ -67,10 +67,10 @@ + style="fill:#f9f9f9;fill-opacity:1"> tutorial ## Prerequisites diff --git a/docs/usage.md b/docs/usage.md index 4827056..4f462c0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# usage reference +# usage reference `geofetch` command-line usage instructions: @@ -9,7 +9,7 @@ usage: geofetch [-h] -i INPUT [-n NAME] [-m METADATA_FOLDER] [-f] [--just-metadata] [-r] [--acc-anno] [--use-key-subset] [-x] [--config-template CONFIG_TEMPLATE] [-p] [-g GEO_FOLDER] - [-b BAM_FOLDER] + [-b BAM_FOLDER] [-P PIPELINE_INTERFACES] Automatic GEO SRA data downloader @@ -40,7 +40,7 @@ optional arguments: setting instead treats each run as a separate sample --config-template CONFIG_TEMPLATE Project config yaml file template. - -p, --processed Download processed data (Default: download raw data). + -p, --processed Download processed data [Default: download raw data]. -g GEO_FOLDER, --geo-folder GEO_FOLDER Optional: Specify a location to store processed GEO files [Default: $GEODATA:] @@ -48,4 +48,7 @@ optional arguments: Optional: Specify folder of bam files. Geofetch will not download sra files when corresponding bam files already exist. [Default: $SRABAM:] + -P PIPELINE_INTERFACES, --pipeline_interfaces PIPELINE_INTERFACES + Optional: Specify the filepath of a pipeline interface + yaml file. [Default: null] ``` diff --git a/docs/usage_template.md b/docs/usage_template.md index 39dedaa..ac6a28f 100644 --- a/docs/usage_template.md +++ b/docs/usage_template.md @@ -1,4 +1,4 @@ -# usage reference +# usage reference `geofetch` command-line usage instructions: diff --git a/mkdocs.yml b/mkdocs.yml index 628bfae..d64b0f1 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -13,6 +13,7 @@ nav: - How to control data location: howto-location.md - Reference: - Usage: usage.md + - FAQ: faq.md - Support: support.md - Contributing: contributing.md - Changelog: changelog.md diff --git a/setup.py b/setup.py index 9916e0e..ca8bd07 100644 --- a/setup.py +++ b/setup.py @@ -56,7 +56,7 @@ def get_static(name, condition=None): name=PACKAGE, packages=[PACKAGE], version=version, - description="A ", + description="Downloads data and metadata from GEO and SRA and creates standard PEPs.", long_description=long_description, classifiers=[ "Development Status :: 4 - Beta",