From 40a82fb971468b235c71b17bad05f7ec38afd7ad Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Wed, 31 May 2023 07:42:52 +0000 Subject: automatic import of python-cg-fluffy --- .gitignore | 1 + python-cg-fluffy.spec | 437 ++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 439 insertions(+) create mode 100644 python-cg-fluffy.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..841ed5f 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/cg-fluffy-3.2.0.tar.gz diff --git a/python-cg-fluffy.spec b/python-cg-fluffy.spec new file mode 100644 index 0000000..37bf9fe --- /dev/null +++ b/python-cg-fluffy.spec @@ -0,0 +1,437 @@ +%global _empty_manifest_terminate_build 0 +Name: python-cg-fluffy +Version: 3.2.0 +Release: 1 +Summary: NIPT analysis pipeline +License: MIT +URL: https://github.com/Clinical-Genomics/fluffy +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4b/1d/29e5a919194598b9befab33f602c8711b330b02de20bd13b02b2551e623a/cg-fluffy-3.2.0.tar.gz +BuildArch: noarch + +Requires: python3-click +Requires: python3-coloredlogs +Requires: python3-slurmpy +Requires: python3-pyyaml +Requires: python3-numpy + +%description + +![Build](https://github.com/Clinical-Genomics/fluffy/workflows/Build/badge.svg) +[![codecov](https://codecov.io/gh/Clinical-Genomics/fluffy/branch/master/graph/badge.svg)](https://codecov.io/gh/Clinical-Genomics/fluffy) +# FluFFyPipe +NIPT analysis pipeline, using WisecondorX for detecting aneuplodies and large CNVs, AMYCNE for FFY and PREFACE for FF prediction (optional). FluFFYPipe produces a variety of output files, as well as a per batch csv summary. + +

+ +

+ +# Run FluFFyPipe +Run NIPT analysis, using a previously comnputed reference: + + fluffy --sample --project --out --analyse + +Run NIPT analysis, using an internally computed reference (i.e the reference is built using all samples listed in samplesheet): + + fluffy --sample --project --out --analyse --batch-ref + +optionally, skip preface: + + fluffy --sample --project --out --skip_preface --analyse + +All output will be written to the output folder, this output includes: + +``` +bam files +wisecondorX output +tiddit coverage summary +Fetal fraction estimation +``` + +as well as a summary csv and multiqc html (per batch) + +the input folder is a project folder containing one folder per sample, each of these subfolders contain the fastq file(s). +The samplesheet contains at least a "sampleID" column, the sampleID should match the subfolders in the input folder. The samplesheet may contain other columns, such as flowcell and index folder: such columns will be printed to the summary csv. +If the samplesheet contains a SampleName column, fluffy will name the output according to SampleName + +Create a WisecondorX reference + + fluffy --sample --project --out --reference + +samplesheet should contain atleast a "sampleID" column. All samples in the samplesheet will be used to construct the reference, visit the WisecondorX manual for more information. +# Optional fluffy parameters: + Analysis mode: + --dry_run - run the pipeline without generating files + -l - add paramters to the slurm header of the script, should be given on the following format parameter:value + example: qos:high + + Reference mode: + --dry_run - run the pipeline without generating files + + Rerun mode: + --dry_run - run the pipeline without generating files + +# Troubleshooting and rerun +There are three statuses of the fluffy pipeline: +running, complete, and failed + +The status of a fluffy run is found in the + + /analysis_status.json + +The status of all jobs are listed in + + /sacct/fluffy_.log.status + +Where is the timepoint when the jobs were submitted +Use grep to find the failed jobs: + + grep -v COMPLETE /sacct/fluffy_.log.status + +The output logs are stored in: + + /logs + +Before continuing, you may want to generate the summary csv for all completed cases: + + bash /scripts/summarizebatch- + +where is a randomly generated string. + +use the rerun module to rerun failed fluffy analyses: + + fluffy --sample --project --out --skip_preface rerun + + +# Install FluFFyPipe +FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs. + +fluffy may be installed using pip: + + pip install fluffy-cg + +alternatively, fluffy is cloned and installed from github: + git clone https://github.com/Clinical-Genomics/fluffy + cd fluffy + pip install -e . + +Next download the FluFFyPipe singularity container + + singularity pull library://jeisfeldt/default/fluffy:sha256.dbef92cd5eab8558c2729f73a191d73a7576a24e9bb44dde7372c0cd405c4ef6 + +copy the example config (found in example_config), and edit the variables. +You will need to download/create the following files: + + Reference fasta (indexed using bwa) + + WisecondorX reference files (created using the reference mode) + + PREFACE model file (optional) + + blacklist bed file (used by wisecondorX) + + FluFFyPipe singularity collection (singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe) + + + + + + + +%package -n python3-cg-fluffy +Summary: NIPT analysis pipeline +Provides: python-cg-fluffy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-cg-fluffy + +![Build](https://github.com/Clinical-Genomics/fluffy/workflows/Build/badge.svg) +[![codecov](https://codecov.io/gh/Clinical-Genomics/fluffy/branch/master/graph/badge.svg)](https://codecov.io/gh/Clinical-Genomics/fluffy) +# FluFFyPipe +NIPT analysis pipeline, using WisecondorX for detecting aneuplodies and large CNVs, AMYCNE for FFY and PREFACE for FF prediction (optional). FluFFYPipe produces a variety of output files, as well as a per batch csv summary. + +

+ +

+ +# Run FluFFyPipe +Run NIPT analysis, using a previously comnputed reference: + + fluffy --sample --project --out --analyse + +Run NIPT analysis, using an internally computed reference (i.e the reference is built using all samples listed in samplesheet): + + fluffy --sample --project --out --analyse --batch-ref + +optionally, skip preface: + + fluffy --sample --project --out --skip_preface --analyse + +All output will be written to the output folder, this output includes: + +``` +bam files +wisecondorX output +tiddit coverage summary +Fetal fraction estimation +``` + +as well as a summary csv and multiqc html (per batch) + +the input folder is a project folder containing one folder per sample, each of these subfolders contain the fastq file(s). +The samplesheet contains at least a "sampleID" column, the sampleID should match the subfolders in the input folder. The samplesheet may contain other columns, such as flowcell and index folder: such columns will be printed to the summary csv. +If the samplesheet contains a SampleName column, fluffy will name the output according to SampleName + +Create a WisecondorX reference + + fluffy --sample --project --out --reference + +samplesheet should contain atleast a "sampleID" column. All samples in the samplesheet will be used to construct the reference, visit the WisecondorX manual for more information. +# Optional fluffy parameters: + Analysis mode: + --dry_run - run the pipeline without generating files + -l - add paramters to the slurm header of the script, should be given on the following format parameter:value + example: qos:high + + Reference mode: + --dry_run - run the pipeline without generating files + + Rerun mode: + --dry_run - run the pipeline without generating files + +# Troubleshooting and rerun +There are three statuses of the fluffy pipeline: +running, complete, and failed + +The status of a fluffy run is found in the + + /analysis_status.json + +The status of all jobs are listed in + + /sacct/fluffy_.log.status + +Where is the timepoint when the jobs were submitted +Use grep to find the failed jobs: + + grep -v COMPLETE /sacct/fluffy_.log.status + +The output logs are stored in: + + /logs + +Before continuing, you may want to generate the summary csv for all completed cases: + + bash /scripts/summarizebatch- + +where is a randomly generated string. + +use the rerun module to rerun failed fluffy analyses: + + fluffy --sample --project --out --skip_preface rerun + + +# Install FluFFyPipe +FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs. + +fluffy may be installed using pip: + + pip install fluffy-cg + +alternatively, fluffy is cloned and installed from github: + git clone https://github.com/Clinical-Genomics/fluffy + cd fluffy + pip install -e . + +Next download the FluFFyPipe singularity container + + singularity pull library://jeisfeldt/default/fluffy:sha256.dbef92cd5eab8558c2729f73a191d73a7576a24e9bb44dde7372c0cd405c4ef6 + +copy the example config (found in example_config), and edit the variables. +You will need to download/create the following files: + + Reference fasta (indexed using bwa) + + WisecondorX reference files (created using the reference mode) + + PREFACE model file (optional) + + blacklist bed file (used by wisecondorX) + + FluFFyPipe singularity collection (singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe) + + + + + + + +%package help +Summary: Development documents and examples for cg-fluffy +Provides: python3-cg-fluffy-doc +%description help + +![Build](https://github.com/Clinical-Genomics/fluffy/workflows/Build/badge.svg) +[![codecov](https://codecov.io/gh/Clinical-Genomics/fluffy/branch/master/graph/badge.svg)](https://codecov.io/gh/Clinical-Genomics/fluffy) +# FluFFyPipe +NIPT analysis pipeline, using WisecondorX for detecting aneuplodies and large CNVs, AMYCNE for FFY and PREFACE for FF prediction (optional). FluFFYPipe produces a variety of output files, as well as a per batch csv summary. + +

+ +

+ +# Run FluFFyPipe +Run NIPT analysis, using a previously comnputed reference: + + fluffy --sample --project --out --analyse + +Run NIPT analysis, using an internally computed reference (i.e the reference is built using all samples listed in samplesheet): + + fluffy --sample --project --out --analyse --batch-ref + +optionally, skip preface: + + fluffy --sample --project --out --skip_preface --analyse + +All output will be written to the output folder, this output includes: + +``` +bam files +wisecondorX output +tiddit coverage summary +Fetal fraction estimation +``` + +as well as a summary csv and multiqc html (per batch) + +the input folder is a project folder containing one folder per sample, each of these subfolders contain the fastq file(s). +The samplesheet contains at least a "sampleID" column, the sampleID should match the subfolders in the input folder. The samplesheet may contain other columns, such as flowcell and index folder: such columns will be printed to the summary csv. +If the samplesheet contains a SampleName column, fluffy will name the output according to SampleName + +Create a WisecondorX reference + + fluffy --sample --project --out --reference + +samplesheet should contain atleast a "sampleID" column. All samples in the samplesheet will be used to construct the reference, visit the WisecondorX manual for more information. +# Optional fluffy parameters: + Analysis mode: + --dry_run - run the pipeline without generating files + -l - add paramters to the slurm header of the script, should be given on the following format parameter:value + example: qos:high + + Reference mode: + --dry_run - run the pipeline without generating files + + Rerun mode: + --dry_run - run the pipeline without generating files + +# Troubleshooting and rerun +There are three statuses of the fluffy pipeline: +running, complete, and failed + +The status of a fluffy run is found in the + + /analysis_status.json + +The status of all jobs are listed in + + /sacct/fluffy_.log.status + +Where is the timepoint when the jobs were submitted +Use grep to find the failed jobs: + + grep -v COMPLETE /sacct/fluffy_.log.status + +The output logs are stored in: + + /logs + +Before continuing, you may want to generate the summary csv for all completed cases: + + bash /scripts/summarizebatch- + +where is a randomly generated string. + +use the rerun module to rerun failed fluffy analyses: + + fluffy --sample --project --out --skip_preface rerun + + +# Install FluFFyPipe +FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs. + +fluffy may be installed using pip: + + pip install fluffy-cg + +alternatively, fluffy is cloned and installed from github: + git clone https://github.com/Clinical-Genomics/fluffy + cd fluffy + pip install -e . + +Next download the FluFFyPipe singularity container + + singularity pull library://jeisfeldt/default/fluffy:sha256.dbef92cd5eab8558c2729f73a191d73a7576a24e9bb44dde7372c0cd405c4ef6 + +copy the example config (found in example_config), and edit the variables. +You will need to download/create the following files: + + Reference fasta (indexed using bwa) + + WisecondorX reference files (created using the reference mode) + + PREFACE model file (optional) + + blacklist bed file (used by wisecondorX) + + FluFFyPipe singularity collection (singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe) + + + + + + + +%prep +%autosetup -n cg-fluffy-3.2.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-cg-fluffy -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot - 3.2.0-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..b0dcdc4 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +9053feafa62ac022ddec1a211051f926 cg-fluffy-3.2.0.tar.gz -- cgit v1.2.3