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Merge branch 'master' of github.com:lskatz/Kalamari
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lskatz committed Dec 31, 2024
2 parents 9d8750f + e75b9e7 commit 9947483
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47 changes: 47 additions & 0 deletions .github/workflows/draft-docx.yml.bak
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on:
push:
paths:
- 'paper/**'
- '.github/workflows/draft-docx.yml'

name: JOSS docx rendering
env:
OPENJOURNALS_PATH: /usr/local/share/openjournals
format: docx
article_info_option: ""

jobs:
paper:
runs-on: ubuntu-latest
name: Paper Draft
container:
image: openjournals/inara:latest
env:
GIT_SHA: $GITHUB_SHA
JOURNAL: joss
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Build draft docx
# inara -o docx paper/paper.md
run: |
/usr/local/bin/pandoc \
--data-dir="${{ env.OPENJOURNALS_PATH }}/data" \
--defaults="${{ env.OPENJOURNALS_PATH }}/${{ env.format }}/defaults.yaml" \
${{ env.article_info_option}} \
--resource-path=.:${{ env.OPENJOURNALS_PATH }}/scripts \
--variable="${{ env.JOURNAL }}" \
--variable=retraction:"${{ env.retraction }}" \
--variable=draft:"${{ env.draft }}" \
--metadata=draft:"${{ env.draft }}" \
--log="$logfile" \
"$input_file" \
"$@"
- name: Upload
uses: actions/upload-artifact@v4
with:
name: paper
# This is the output path where Pandoc will write the compiled
# PDF. Note, this should be the same directory as the input
# paper.md
path: paper/paper.docx
29 changes: 29 additions & 0 deletions .github/workflows/draft-pdf.yml
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on:
push:
paths:
- 'paper/**'
- '.github/workflows/draft-pdf.yml'

name: JOSS pdf rendering

jobs:
paper:
runs-on: ubuntu-latest
name: Paper Draft
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Build draft PDF
uses: openjournals/openjournals-draft-action@master
with:
journal: joss
# This should be the path to the paper within your repo.
paper-path: paper/paper.md
- name: Upload
uses: actions/upload-artifact@v4
with:
name: paper
# This is the output path where Pandoc will write the compiled
# PDF. Note, this should be the same directory as the input
# paper.md
path: paper/paper.pdf
3 changes: 2 additions & 1 deletion .github/workflows/unit-testing.Listeria.Kraken1.yml
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# This is a subsampling unit test to get early results
on:
push:
branches: [master, dev]
branches: [master, dev, validate-taxonomy]
pull_request:
name: Listeria-with-Kraken1

env:
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5 changes: 2 additions & 3 deletions .github/workflows/unit-testing.Yersinia.Kraken2.yml
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# This is a subsampling unit test to get early results
on:
push:
branches: [master, dev]
branches: [master, dev, validate-taxonomy]
pull_request:
name: Genera-with-Kraken2

env:
Expand Down Expand Up @@ -34,14 +35,12 @@ jobs:
- name: env check
run: |
echo $PATH | tr ':' '\n' | sort
- name: install-edirect
run: |
sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
echo $HOME/edirect >> $GITHUB_PATH
echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH
tree $HOME/edirect
- name: apt-get install
run: sudo apt-get install ca-certificates tree jellyfish ncbi-entrez-direct
- name: select for only for this genus
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4 changes: 2 additions & 2 deletions .github/workflows/unit-testing.yml
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@@ -1,6 +1,7 @@
on:
push:
branches: [master, dev]
branches: [master, dev, validate-taxonomy]
pull_request:
name: Pull-down-all-accessions

jobs:
Expand All @@ -25,7 +26,6 @@ jobs:

- name: apt-get install
run: sudo apt-get install ca-certificates tree

- name: install-edirect
run: |
sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
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1 change: 1 addition & 0 deletions .github/workflows/validateTaxonomy.yml
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@@ -1,6 +1,7 @@
on:
push:
branches: [master, dev, esearch-input]
pull_request:
name: Validate taxonomy

jobs:
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5 changes: 5 additions & 0 deletions .gitignore
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edirect
share
paper/paper.html
paper/paper.doc
# pixi environments
.pixi
*.egg-info
9 changes: 5 additions & 4 deletions README.md
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# Kalamari
A database of completed assemblies for metagenomics-related tasks

## Synopsis

Expand All @@ -9,12 +8,14 @@ These assemblies can be further used in formatted databases such as Kraken or Bl
### Prerequisites & Recommendations

Requirements:

- clone this repo locally `git clone https://github.com/lskatz/Kalamari.git`
- NCBI entrez-utilities set of tools `edirect`, `esearch`, etc.
- install via your package manager
- debian/ubuntu: `apt install ncbi-entrez-direct`
- debian/ubuntu: `apt install ncbi-entrez-direct`

Optional, but recommended:

- `NCBI_API_KEY` environmental variable
- `EMAIL` environmental variable

Expand All @@ -27,12 +28,12 @@ After obtaining an NCBI API key, add it to your environment with

where `unique_api_key_goes_here` is a unique hexadecimal number with characters from 0-9 and a-f.

You should also set your email address in the
You should also set your email address in the
`EMAIL` environment variable as edirect tries to guess it, which is an error prone process.
Add this variable to your environment with

export EMAIL=my@email.address

using your own email address instead of `my@email.address`.

## Download instructions
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1 change: 0 additions & 1 deletion bin/buildKraken1.sh
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Expand Up @@ -40,7 +40,6 @@ kraken-build --db $DB --build --threads 1
# Reduce the size of the database
kraken-build --db $DB --clean


if [ ! -e "$sharedir/kalamari-kraken1" ]; then
ln -sv kalamari-kraken "$sharedir/kalamari-kraken1"
fi
175 changes: 175 additions & 0 deletions paper/asm.csl
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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
<info>
<title>American Society for Microbiology</title>
<title-short>ASM</title-short>
<id>http://www.zotero.org/styles/american-society-for-microbiology</id>
<link href="http://www.zotero.org/styles/american-society-for-microbiology" rel="self"/>
<link href="https://journals.asm.org/references" rel="documentation"/>
<author>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</author>
<contributor>
<name>Rintze Zelle</name>
<uri>http://twitter.com/rintzezelle</uri>
</contributor>
<contributor>
<name>Richard Karnesky</name>
<email>karnesky+zotero@gmail.com</email>
<uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
</contributor>
<contributor>
<name>Charles Parnot</name>
<uri>http://twitter.com/cparnot</uri>
<email>charles.parnot@gmail.com</email>
</contributor>
<contributor>
<name>Patrick O'Brien</name>
</contributor>
<category citation-format="numeric"/>
<category field="biology"/>
<summary>Style for all American Society for Microbiology journals.</summary>
<updated>2022-01-22T01:10:09+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="author">
<names variable="author" suffix=".">
<name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
</names>
</macro>
<macro name="issued">
<group prefix=" " suffix=".">
<choose>
<if type="patent">
<date variable="issued">
<date-part name="month" suffix=" "/>
<date-part name="year"/>
</date>
</if>
<else>
<date variable="issued">
<date-part name="year"/>
</date>
</else>
</choose>
</group>
</macro>
<macro name="chapter-specifics">
<choose>
<if type="chapter paper-conference" match="any">
<label variable="page" form="short" plural="never" prefix=", " suffix=" "/>
<text variable="page"/>
<text term="in" text-case="capitalize-first" prefix=". " suffix=" " font-style="italic"/>
<names variable="editor" delimiter=", " suffix=", ">
<name initialize-with="" delimiter=", " name-as-sort-order="all" delimiter-precedes-last="always"/>
<label form="short" prefix=" (" suffix=")"/>
</names>
</if>
</choose>
</macro>
<macro name="patent-specifics">
<text variable="number" prefix=". "/>
</macro>
<macro name="container-title">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
<text variable="container-title"/>
</if>
<else>
<text variable="container-title" form="short" strip-periods="true" prefix=". "/>
</else>
</choose>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" " prefix=", ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<macro name="publisher">
<choose>
<if type="article-journal article-magazine" match="none">
<group delimiter=". " prefix=". ">
<choose>
<if type="book" match="none">
<text variable="genre"/>
</if>
</choose>
<group delimiter=", ">
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</group>
</if>
</choose>
</macro>
<macro name="locators">
<choose>
<if type="article-journal">
<choose>
<if match="none" variable="volume page">
<text variable="DOI" prefix=" https://doi.org/"/>
</if>
<else>
<group prefix=" " delimiter=":">
<text variable="volume"/>
<text variable="page"/>
</group>
</else>
</choose>
</if>
<else-if type="article">
<text variable="DOI" prefix=" https://doi.org/"/>
</else-if>
<else-if type="book webpage post post-weblog" match="any">
<group delimiter=". " prefix=". ">
<text variable="URL"/>
<group delimiter=" ">
<text term="retrieved" text-case="capitalize-first"/>
<date variable="accessed">
<date-part name="day"/>
<date-part name="month" prefix=" "/>
<date-part name="year" prefix=" "/>
</date>
</group>
</group>
</else-if>
</choose>
</macro>
<macro name="title">
<group delimiter=" ">
<text variable="title"/>
<text variable="version" prefix="(" suffix=")"/>
</group>
</macro>
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout prefix="(" suffix=")" delimiter=", ">
<text variable="citation-number"/>
</layout>
</citation>
<bibliography entry-spacing="1" line-spacing="2" second-field-align="flush">
<layout suffix=".">
<text variable="citation-number" suffix=". "/>
<text macro="author"/>
<text macro="issued"/>
<text macro="title" prefix=" "/>
<text macro="chapter-specifics"/>
<text macro="patent-specifics"/>
<text macro="container-title"/>
<text macro="edition"/>
<text macro="publisher"/>
<text macro="locators"/>
</layout>
</bibliography>
</style>
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