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pulling in changes from the master branch #56

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30bfb4b
Install basespace CLI
arisp99 Oct 29, 2021
8256cac
Added default options and settings
AshlinHarris Nov 1, 2021
9683580
Remove old python download script
arisp99 Nov 1, 2021
4291393
Define basespace download app
arisp99 Nov 1, 2021
cf7e317
Add help page
arisp99 Nov 1, 2021
b67ffaf
Add template basespace authentication file
arisp99 Nov 1, 2021
d87cd34
Add -h as a flag
arisp99 Nov 1, 2021
2fa35ed
Add an example to help page
arisp99 Nov 1, 2021
f95b6a3
Format code
arisp99 Nov 2, 2021
83b58dd
Don't require both `/opt/data` and `/opt/analysis`
arisp99 Nov 2, 2021
8f5e9a7
Style code
arisp99 Nov 2, 2021
5e9921e
Update changelog
arisp99 Nov 2, 2021
6ff787e
Improve docs for `demux_qc` app
arisp99 Nov 3, 2021
b43b732
Style code
arisp99 Nov 3, 2021
e51f3d2
Update `.gitignore`
arisp99 Nov 3, 2021
438a36b
Merge remote-tracking branch 'origin/master'
arisp99 Nov 3, 2021
7d4ecdb
Merge pull request #13 from arisp99/basespace-download
AshlinHarris Nov 4, 2021
3849118
Revert "Use basespace CLI to download run data" (#14)
arisp99 Nov 4, 2021
b3c76cf
Add `-h` flag for the demux app
arisp99 Nov 4, 2021
1f1da3f
Add `-h` flag to the download app
arisp99 Nov 4, 2021
d478ac8
Add `-h` flag to wrangler app
arisp99 Nov 4, 2021
c385952
Add `-h` flag to the jupyter app
arisp99 Nov 6, 2021
600121f
Style code
arisp99 Nov 6, 2021
cc84f66
Modify project version and add doc badge
arisp99 Nov 6, 2021
796563e
Add basic web documentation
arisp99 Nov 6, 2021
7b9c9e5
Remove extension
arisp99 Nov 6, 2021
e9af391
Update installation.rst
JeffAndBailey Nov 7, 2021
888a382
Use Github Pages to deploy docs
arisp99 Nov 8, 2021
c57f8b9
Allow for docs to be written in MyST
arisp99 Nov 8, 2021
3cd3c42
Update README
arisp99 Nov 8, 2021
a675a9d
Add edit on github link
arisp99 Nov 8, 2021
0aa7253
Add copy button to code chunks
arisp99 Nov 8, 2021
9447637
Update changelog
arisp99 Nov 8, 2021
83e3bd2
Fix docs workflow
arisp99 Nov 8, 2021
4d3fe44
Add issue templates
arisp99 Nov 10, 2021
98d810a
Update issue templates
arisp99 Nov 10, 2021
b403d6a
Update issue templates
arisp99 Nov 10, 2021
e0b3d79
Update deploy docs workflow
arisp99 Nov 15, 2021
2bdd801
Change frequency of reminder
arisp99 Dec 15, 2021
73cf66b
Don't deploy to `gh-pages` on PRs
arisp99 Dec 15, 2021
0354b79
Update license
arisp99 Feb 6, 2022
fb6ab02
Remove dev definition file
arisp99 Feb 6, 2022
776e355
Update to sample sheet preparation addressing some issues arising fro…
aydemiro Feb 14, 2022
a08e0fd
Update generate_wrangler_scripts.py
aydemiro Feb 14, 2022
0ccd0ad
Install `magrittr` in definition file
arisp99 Feb 15, 2022
9e95177
Reinstall McCOILR
arisp99 Feb 15, 2022
3c0d3a1
Merge pull request #23 from bailey-lab/create-arm-file
JeffAndBailey Feb 21, 2022
2306380
Merge pull request #22 from bailey-lab/samplesheet
JeffAndBailey Feb 21, 2022
26b85ef
Fix version number
arisp99 Feb 21, 2022
5007b89
Remove miscellaneous audio file
arisp99 Feb 22, 2022
f34b82d
Store a single README
arisp99 Feb 22, 2022
40d42ee
Update changelog
arisp99 Feb 25, 2022
e1abfce
Supersede python download app
arisp99 Feb 25, 2022
8b7acde
Install basespace cli
arisp99 Feb 25, 2022
efb8d61
Define basespace download app
arisp99 Feb 25, 2022
1b43b9f
Download data into a run id subdirectory of output path
arisp99 Feb 25, 2022
a2d407d
Add changelog bullet
arisp99 Feb 25, 2022
1fbf554
Improve check for `run_id` input
arisp99 Feb 25, 2022
1a0fcb7
Add summary flag
arisp99 Feb 25, 2022
508bbe0
Address review comments
arisp99 Feb 28, 2022
1c52025
Fix argument check
arisp99 Feb 28, 2022
ee06b52
Fix help doc
arisp99 Feb 28, 2022
6799d84
Merge pull request #25 from bailey-lab/basespace-download-v2
aydemiro Feb 28, 2022
f7094b1
Update doc versions and clean
arisp99 Feb 28, 2022
305c7b4
Add changelog to docs site
arisp99 Feb 28, 2022
5444bf6
Add docs for the download app
arisp99 Feb 28, 2022
54316a3
Add docs for the superseded download app
arisp99 Feb 28, 2022
76b8c3d
Add demux docs
arisp99 Feb 28, 2022
b5ca31d
Specify missing requirement
arisp99 Feb 28, 2022
48165fc
Fix rst formatting
arisp99 Feb 28, 2022
7ffe98a
Add demux qc docs
arisp99 Mar 1, 2022
fc22a59
Add wrangler app docs
arisp99 Mar 1, 2022
09f52ef
Add jupyter app docs
arisp99 Mar 1, 2022
198cb3b
Remove whitespace from arguments
arisp99 Mar 10, 2022
da94490
Improve docs for `-x` argument of wrangler app
arisp99 Mar 10, 2022
46c9778
Check that arguments are formatted correctly
arisp99 Mar 10, 2022
d43b8dc
Add a contributing section to the README
arisp99 Mar 10, 2022
a589b50
Use a concurrency group for workflow
arisp99 Mar 10, 2022
73ec352
Improve docs and help
arisp99 Mar 11, 2022
2ebeaf7
Point docs to new container download location
arisp99 Mar 11, 2022
61b5fa2
Update the notify maintainers workflow
arisp99 Mar 11, 2022
806c88d
Remove duplicated concurrency group
arisp99 Mar 11, 2022
808926a
Add labels to apps
arisp99 Mar 15, 2022
d3b1a49
Add an FAQ for the jupyter app
arisp99 Mar 15, 2022
69ff95f
Add an example analysis run using the test data
arisp99 Mar 15, 2022
0a3aa34
Add instructions on using singularity to run MIPTools
arisp99 Mar 15, 2022
2ba12aa
Add a simple probe design guide
arisp99 Mar 15, 2022
1a37cd8
Change guide name
arisp99 Mar 15, 2022
515276d
Fix code highlighting
arisp99 Mar 16, 2022
06ff57f
Style, improve clarity, reorder arguments to match function
arisp99 Mar 21, 2022
8c841ba
Set default number of threads to 20
arisp99 Mar 21, 2022
4a03d73
Let Freebayes run with only one CPU thread
arisp99 Mar 21, 2022
097474b
Use URL instead of sphinx-toolbox
arisp99 Mar 21, 2022
a67b4b9
Add license, source code links, and 404 page
arisp99 Mar 22, 2022
4fec0ce
Downgrade sphinx version so extensions work
arisp99 Mar 22, 2022
b4ad24d
Fix build container script
arisp99 Apr 4, 2022
f2efdb9
Don't store source code for programs (#36)
arisp99 Apr 26, 2022
a2eb4bc
Install mipscripts
arisp99 Apr 26, 2022
ea30dfd
Add a guide on HPCC use
arisp99 Apr 27, 2022
d3e613c
Update changelog
arisp99 Apr 27, 2022
cf92a59
Don't use parameter expansion as it is non-POSIX
arisp99 Apr 27, 2022
921a9c9
Update bug report template
arisp99 Apr 29, 2022
ecf35f5
Don't install `libgfortran4`
arisp99 Apr 30, 2022
16af5c2
Merge remote-tracking branch 'origin/master'
arisp99 Apr 30, 2022
32ca3d4
Update changelog
arisp99 Apr 30, 2022
ddd5f3b
Remove unused analysis settings files
arisp99 May 2, 2022
5ebaf36
Remove sequence aligners and functions
arisp99 May 2, 2022
c4001d2
Specify version number for installed software (#32)
arisp99 May 2, 2022
26eca75
Only save installed binaries of programs
arisp99 May 2, 2022
b65c063
Remove `msa2vcf` program and other conversion files
arisp99 May 4, 2022
4d87dd6
Style generate wrangler script
arisp99 May 6, 2022
8c68591
Change channel priority and remove default channel
arisp99 May 6, 2022
06b03a0
Alphabetize packages and install quietly
arisp99 May 6, 2022
b628033
Fix rm statement as software is no longer installed
arisp99 May 6, 2022
095d111
Remove `msa_to_vcf` module
arisp99 May 6, 2022
4376805
Don't remove `MIPWrangler` and `elucidator` source code
arisp99 May 9, 2022
25ef3b9
Add a population clustering fraction cutoff argument (#39)
arisp99 May 9, 2022
a51dec5
Combine the two `nohup.out` files and force the mv command
arisp99 May 9, 2022
6ccdf46
Update changelog
arisp99 May 10, 2022
8e3ed00
Install mipscripts from pip
arisp99 May 13, 2022
18bdb8e
Improve docs
arisp99 Jun 14, 2022
0f3bc92
Downsample UMI counts (#40)
arisp99 Jun 14, 2022
f0a8094
Correct port forwarding command
arisp99 Jun 22, 2022
44ca536
Update package version and install plotnine
arisp99 Aug 7, 2022
398d130
Install C and C++ compiler version 10
arisp99 Aug 10, 2022
7623589
Remove singularity build badge
arisp99 Aug 10, 2022
ea27d4d
Edit punctuation (#44)
asimkinbrown Nov 18, 2022
89a4c12
Temporarily mute workflow to notify maintainers
arisp99 Dec 5, 2022
3825bea
Add new workflow for deploying production docs
arisp99 Dec 6, 2022
4b0f96b
Deploy to new gh-pages site
arisp99 Dec 6, 2022
e70661a
point to working jupyter file
asimkinbrown Dec 7, 2022
ae40c7b
point to correct mip file
asimkinbrown Dec 7, 2022
4bc8798
editing wrong branch
asimkinbrown Dec 7, 2022
7a3d60f
Add maintenance issue template
arisp99 Jan 5, 2023
c1d8040
Remove GitHub pages documentation workflows and update README badge
arisp99 Jan 5, 2023
993bb72
Fix flag for demux qc app and update license year
arisp99 Jan 5, 2023
677c6ef
Update copyright year
arisp99 Jan 5, 2023
8531b35
remove analysis_template_with_qual.ipynb filters
asimkinbrown Apr 7, 2023
a31e3e9
updating Jupyter notebooks
alfredsimkin Jun 15, 2023
b4c5c47
Update sample_sheet_prep.py
aydemiro Sep 26, 2023
a76529f
added check_run_stats
alfredsimkin Jun 15, 2023
5ca134c
keep only relevant cells
alfredsimkin Jun 15, 2023
0f22bf4
removed sample sheet merging attempts
alfredsimkin Jun 15, 2023
6670d82
added back species variable
alfredsimkin Jun 16, 2023
8300e7d
fixed Jupyter ulimit bug, bwa_multi bug
alfredsimkin Jul 11, 2023
844aa13
added freebayes threads to notebook
alfredsimkin Jul 12, 2023
d0428d4
fixed freebayes tab
alfredsimkin Jul 12, 2023
78c39da
remove duplicate line
alfredsimkin Jul 12, 2023
5bc5397
system-wide ulimit, PYTHONNOUSERSITE
alfredsimkin Jul 18, 2023
d21ae24
ulimit tinkering
alfredsimkin Jul 18, 2023
a9e1ccc
set MIPWrangler branch to develop
alfredsimkin Aug 14, 2023
005827f
installing jupyter_contrib_nbextensions with git
alfredsimkin Aug 15, 2023
cf69fa2
nb_convert now regular pip
alfredsimkin Aug 22, 2023
67fd777
setting versioned environment
alfredsimkin Aug 25, 2023
2a86293
setting versioned environment
alfredsimkin Aug 25, 2023
faa49ed
wrangler output zipped
alfredsimkin Sep 12, 2023
21ef3a8
fixed copying of final zipped files
alfredsimkin Sep 15, 2023
bc22a99
charlie new mip functions
alfredsimkin Jan 4, 2024
db3cfcf
write filters to csv files
alfredsimkin Jan 4, 2024
cae0b8c
added pool to Jupyter notebook
alfredsimkin Jan 4, 2024
d067ef6
freebayes_worker compat w freebayes_call
alfredsimkin Jan 4, 2024
6613c18
jupyter compat w freebayes_worker
alfredsimkin Jan 4, 2024
bc1ea00
commented in error tracking
alfredsimkin Jan 4, 2024
81d98fb
added snakemake folder
charliesimkin Jan 5, 2024
9460f01
add pip and snakemake to the def file
charliesimkin Jan 5, 2024
91d2e71
get generate contigs working
charliesimkin Jan 5, 2024
304453a
get run freebayes working
charliesimkin Jan 5, 2024
aff9fa5
added snakemake folder
charliesimkin Jan 5, 2024
aa50623
add pip and snakemake to the def file
charliesimkin Jan 5, 2024
ef4d138
get generate contigs working
charliesimkin Jan 5, 2024
5977dd7
get run freebayes working
charliesimkin Jan 5, 2024
31015a7
Merge pull request #51 from bailey-lab/snakemake_in_sif
alfredsimkin Jan 6, 2024
4d1f460
added user scripts
charliesimkin Jan 6, 2024
1bea547
adding updated sif home directory
alfredsimkin Jan 8, 2024
a682f9d
snakemake copy file fixes
alfredsimkin Jan 8, 2024
92ca23b
added files
Jan 11, 2024
27cc70b
updated yaml
charliesimkin Jan 11, 2024
b23bec2
shell script bindings set up
charliesimkin Jan 11, 2024
f1364d0
got the setup working
charliesimkin Jan 11, 2024
9ff981a
got the finish working
charliesimkin Jan 11, 2024
46bdeaf
removed the snakemake bindings after new sif built
charliesimkin Jan 11, 2024
fe145eb
updated the method for entering sample sheet path
charliesimkin Jan 11, 2024
552bfe5
added check run stats
charliesimkin Jan 11, 2024
dbffab0
a readme note in check run stats
charliesimkin Jan 11, 2024
e9d9e05
fix copy params
charliesimkin Jan 11, 2024
c12a7e0
fix copy params
charliesimkin Jan 11, 2024
ded8e51
updated readme in user scripts
charliesimkin Jan 11, 2024
1b9c975
new mip_function concatenate_headers
alfredsimkin Jan 24, 2024
f509dcd
better passing of vcf paths
alfredsimkin Jan 24, 2024
cfbdb12
updated yamls
alfredsimkin Feb 3, 2024
50bf2be
fixing up notebook
alfredsimkin Feb 3, 2024
cb6e1de
updated intro docs
alfredsimkin Feb 6, 2024
494179a
updated intro formatting
alfredsimkin Feb 6, 2024
a30919d
updated intro formatting
alfredsimkin Feb 6, 2024
f19bcef
more intro formatting
alfredsimkin Feb 6, 2024
fdf0d61
more intro formatting
alfredsimkin Feb 6, 2024
8578fe9
Merge branch 'v0.4.0-prod-docs' into temp_branch
alfredsimkin Feb 6, 2024
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Define basespace download app
  • Loading branch information
arisp99 committed Feb 25, 2022
commit efb8d61b93bf5c729d3ab2e80641dd224f169e15
69 changes: 68 additions & 1 deletion MIPTools.def
Original file line number Diff line number Diff line change
@@ -396,9 +396,76 @@ From: amd64/ubuntu:20.04
. /opt/analysis/wrangle.sh

##################################################################
## Download App ##
## Basespace Download App ##
##################################################################
%apprun download
# Exit if something fails
set -e

# Set default values for paths
output_path="/opt/analysis"
config_path="/opt/resources/basespace.cfg"

help() {
echo "Download data from the Illumina BaseSpace Sequence Hub."
echo ""
echo "Usage:"
echo " singularity run [options] --app bs_download <container>"\
"[app_options]"
echo ""
echo "Options:"
echo " See 'singularity run'."
echo ""
echo "App Options:"
echo " -i Required. The run ID of the data to download."
echo " -o The path to the output directory."
echo " Default: '/opt/analysis'."
echo " -c The path to the authentication credentials file."
echo " This file is created by 'bs auth'. For additional"
echo " information see the help page for that command."
echo " Default: '/opt/resources/basespace.cfg'."
echo " -h Print the help page."
echo ""
echo "Examples:"
echo " # Set paths"
echo " $ resource_dir=/bin/MIPTools/base_resources"
echo " $ run_dir=/work/usr/example"
echo ""
echo " # Run app"
echo " $ singularity run \\"
echo " -B \$resource_dir:/opt/resources \\"
echo " -B \$run_dir:/opt/analysis \\"
echo " --app bs_download <container> -i <run_id>"
}

# Parse options
while getopts "i:o:c:h" opt; do
case "${opt}" in
c) config_path=${OPTARG} ;;
h) help
exit 1 ;;
i) run_id=${OPTARG} ;;
o) ouput_path=${OPTARG} ;;
*) help
exit 1 ;;
esac
done

# Ensure run_id is specified
if [ ! $run_id ]; then
echo "Argument -i must be provided"
echo "$usage" >&2
exit 1
fi

# Read data from config file
# Remove whitespace from each line and export each line as a variable
export BASESPACE_API_SERVER=$(sed "1q;d" ${config_path} | sed "s/.*=.//g")
export BASESPACE_ACCESS_TOKEN=$(sed "2q;d" ${config_path} | sed "s/.*=.//g")

# Download data
bs download run -i ${run_id} -o ${output_path}

#################################################################
## Superseded Download App ##
#################################################################
2 changes: 2 additions & 0 deletions base_resources/basespace.cfg
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
apiServer = https://api.basespace.illumina.com
accessToken = <access token>