... | @@ -57,9 +57,7 @@ At least one assembly, one library and one database are required. |
... | @@ -57,9 +57,7 @@ At least one assembly, one library and one database are required. |
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# General options
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# General options
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## --library [mandatory]
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## --library [mandatory]
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You can provide fastq files which will be copied to the data directory and be available in the download page.
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You can provide fastq files which will be copied to the data directory and be available in the download page. If the fastq file is not provided, you must use the nb-sequence attribute to populate the database in order to compute the histograms presented in the user interface.
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''If the fastq file is not provided, you must use the nb-sequence attribute to populate the database in order to compute the histograms presented in the user interface.''
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List of available attribute (with * mandatory attribute):
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List of available attribute (with * mandatory attribute):
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* library-name* : [string] the internal library name, must be uniq
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* library-name* : [string] the internal library name, must be uniq
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... | @@ -68,11 +66,11 @@ List of available attribute (with * mandatory attribute): |
... | @@ -68,11 +66,11 @@ List of available attribute (with * mandatory attribute): |
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* tissue : [string] tissue
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* tissue : [string] tissue
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* dev_stage : [string] developpement stage
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* dev_stage : [string] developpement stage
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* type* : [string] library type , available options :
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* type* : [string] library type , available options :
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** se : single end
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* se : single end
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** pe : paired end
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* pe : paired end
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** ose : oriented single end
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* ose : oriented single end
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** ope : oriented paired end
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* ope : oriented paired end
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** mp : mate pair
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* mp : mate pair
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* insert-size : [int] for paired end library you can provide the insert size
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* insert-size : [int] for paired end library you can provide the insert size
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* remark : [string] any comment
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* remark : [string] any comment
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* sequencer : [string] sequencer type
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* sequencer : [string] sequencer type
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... | @@ -83,15 +81,14 @@ List of available attribute (with * mandatory attribute): |
... | @@ -83,15 +81,14 @@ List of available attribute (with * mandatory attribute): |
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* files* : [string] fastq file path ( if paired space separate file names)
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* files* : [string] fastq file path ( if paired space separate file names)
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If you have several library you have to use the library option several times.
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If you have several library you have to use the library option several times.
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Example :
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Example :
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```bash
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--library library-name=brain_400 sample-name=Brain replicat=1 tissue=Brain type=pe insert-size=400 remark="100bp to 400bp insert" \
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--library library-name=brain_400 sample-name=Brain replicat=1 tissue=Brain type=pe insert-size=400 remark="100bp to 400bp insert" \
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sequencer=HiSeq2000 files=workflows/rnaseqdenovo/data/brain_400.1.fastq.gz,workflows/rnaseqdenovo/data/brain_400.2.fastq.gz
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sequencer=HiSeq2000 files=workflows/rnaseqdenovo/data/brain_400.1.fastq.gz,workflows/rnaseqdenovo/data/brain_400.2.fastq.gz
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```
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## ASSEMBLY section
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### --assembly [mandatory]
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== ASSEMBLY section ==
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===--assembly [mandatory] ===
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The assembly option is mandatory. The possible attributes are :
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The assembly option is mandatory. The possible attributes are :
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* file* : Fasta file, can be gz.
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* file* : Fasta file, can be gz.
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* software-name* : [string] assembly software name
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* software-name* : [string] assembly software name
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... | @@ -99,20 +96,22 @@ The assembly option is mandatory. The possible attributes are : |
... | @@ -99,20 +96,22 @@ The assembly option is mandatory. The possible attributes are : |
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* software-version* : [string] assembly software version
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* software-version* : [string] assembly software version
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* comments : [string] any comments on this analysis
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* comments : [string] any comments on this analysis
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Example :
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Example :
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```bash
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--assembly file=workflows/rnaseqdenovo/data/contigs.fasta software-name=oases software-parameters="" software-version="0.2.06" comments="Transcript assembly"
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--assembly file=workflows/rnaseqdenovo/data/contigs.fasta software-name=oases software-parameters="" software-version="0.2.06" comments="Transcript assembly"
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```
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### --rename
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=== --rename ===
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Flag to set if you want to rename yours contigs with the gene name of the best annotation.
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Flag to set if you want to rename yours contigs with the gene name of the best annotation.
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=== --prefix ===
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### --prefix
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Prefix value to set for all contig when renaming.
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Prefix value to set for all contig when renaming.
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```bash
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--rename --prefix "GG_"
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--rename --prefix "GG_"
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```
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## ANNOTATION section
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== ANNOTATION section ==
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### --assembly-annot-db [mandatory]
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===--assembly-annot-db [mandatory] ===
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You can provide much as you want databases for annotation with ncbi blast+. The database must have been indexed with makeblastdb.
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You can provide much as you want databases for annotation with ncbi blast+. The database must have been indexed with makeblastdb.
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* file* : Database file (with index in the same directory).
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* file* : Database file (with index in the same directory).
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* type* : [string] kind of data : [genome|nucleic|protein|transcript|unknown]
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* type* : [string] kind of data : [genome|nucleic|protein|transcript|unknown]
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... | @@ -122,39 +121,37 @@ You can provide much as you want databases for annotation with ncbi blast+. The |
... | @@ -122,39 +121,37 @@ You can provide much as you want databases for annotation with ncbi blast+. The |
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* evalue : [float] The maximum e-value for the alignements.
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* evalue : [float] The maximum e-value for the alignements.
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* software : [string] The type of NCBI-Blast+ used for the alignment. [blastx|blastp...] path to exec file is retrieve from PATH or from application.properties.
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* software : [string] The type of NCBI-Blast+ used for the alignment. [blastx|blastp...] path to exec file is retrieve from PATH or from application.properties.
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=== --min-identity ===
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### --min-identity
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option to filter on minimum fraction of identity [0.00-1.00]
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option to filter on minimum fraction of identity [0.00-1.00]
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=== --min-coverage ===
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### --min-coverage
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option to filter on minimum fraction of query coverage [0.00-1.00]
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option to filter on minimum fraction of query coverage [0.00-1.00]
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===--go ===
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### --go
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A GO (Gene Ontology) file enables to associate GO names, evidences ... to each contig
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A GO (Gene Ontology) file enables to associate GO names, evidences ... to each contig
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Example :
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Example :
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```bash
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--go go.txt
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--go go.txt
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```
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More info about [[ go file ]]
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### --skip-rm
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===--skip-rm===
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This option enable to skip repeat masker annotation.
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This option enable to skip repeat masker annotation.
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===--skip-rnammer===
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### --skip-rnammer
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Skip RNAmmer step (RNAmmer is used to add rRNA predictions).
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Skip RNAmmer step (RNAmmer is used to add rRNA predictions).
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===--skip-trna===
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### --skip-trna
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Skip RNAmmer step (RNAmmer is used to add rRNA predictions).
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Skip RNAmmer step (RNAmmer is used to add rRNA predictions).
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## IPRscan section
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==IPRscan section==
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### --skip-iprscan
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===--skip-iprscan===
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This option enable to skip iprscan annotation. Iprscan is long but provide a good annotation for protein domains, ORF, and GO.
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This option enable to skip iprscan annotation. Iprscan is long but provide a good annotation for protein domains, ORF, and GO.
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===--max-orf-nb===
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### --max-orf-nb
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[int] The maximum number of ORF by contig to report in annotation.
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[int] The maximum number of ORF by contig to report in annotation.
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==VARIANT section ==
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## VARIANT section
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===--variant===
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### --variant
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If you perform your own variant detection you can provide the file else the pipeline will detect it with GATK3.
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If you perform your own variant detection you can provide the file else the pipeline will detect it with GATK3.
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This file contains for each the variation informations of the contigs contigs : snps, insertion or deletion. The expected file format is VCF (Variant Calling Format).
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This file contains for each the variation informations of the contigs contigs : snps, insertion or deletion. The expected file format is VCF (Variant Calling Format).
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... | @@ -167,72 +164,71 @@ Here is the list of attributes for this options : |
... | @@ -167,72 +164,71 @@ Here is the list of attributes for this options : |
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* software-version : [string] detection software version
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* software-version : [string] detection software version
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* comments : [string] comments on analysis
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* comments : [string] comments on analysis
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Example :
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Example :
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```bash
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--variant file=variant.vcf software-name=GATK software-parameters="realignement/recalibration/glm BOTH" software-version="v2.4-9-g532efad"
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--variant file=variant.vcf software-name=GATK software-parameters="realignement/recalibration/glm BOTH" software-version="v2.4-9-g532efad"
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```
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===--two-steps-calling''' ===
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### --two-steps-calling
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The SNP calling is realised in two step. The first step (recalibration, calling, filter) has hard filters. The second step (recalibration, calling,
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The SNP calling is realised in two step. The first step (recalibration, calling, filter) has hard filters. The second step (recalibration, calling,
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filter) has standard filters and the variants detected in the first step are used as database of known polymorphic sites.
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filter) has standard filters and the variants detected in the first step are used as database of known polymorphic sites.
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===--variant-annot-db ===
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### --variant-annot-db
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You can use a well known species to annotate your SNP by similarities. You must use a species from Ensembl.
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You can use a well known species to annotate your SNP by similarities. You must use a species from Ensembl.
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* species : the species name for the species used as reference.
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* species : the species name for the species used as reference.
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* fasta : the proteins sequences for the species used as reference.
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* fasta : the proteins sequences for the species used as reference.
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* gtf : the genes and CDS annotations for the species used as reference.
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* gtf : the genes and CDS annotations for the species used as reference.
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* vcf [optional] : known variants for the species used as reference.
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* vcf [optional] : known variants for the species used as reference.
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Example :
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Example :
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```bash
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--variant-annot-db species="Danio rerio" fasta=Danio_rerio.Zv9.pep.all.fa gtf=Danio_rerio.Zv9.77.gtf vcf=Danio_rerio.vcf
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--variant-annot-db species="Danio rerio" fasta=Danio_rerio.Zv9.pep.all.fa gtf=Danio_rerio.Zv9.77.gtf vcf=Danio_rerio.vcf
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```
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=Monitoring workflow=
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# Monitoring workflow
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To get information about all workflows :
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To get information about all workflows :
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```bash
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python ./bin/ngspipelines_cli.py status
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python ./bin/ngspipelines_cli.py status
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```
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To get information about a running workflow
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To get information about a running workflow
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```bash
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python ./bin/ngspipelines_cli.py status --workflow-id XX
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python ./bin/ngspipelines_cli.py status --workflow-id XX
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```
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To get information about workflow errors
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To get information about workflow errors
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```bash
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python ./bin/ngspipelines_cli.py status --workflow-id XX --errors
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python ./bin/ngspipelines_cli.py status --workflow-id XX --errors
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```
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# Delete a project
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=Delete a project=
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The deleteproject option permits to remove a project from an instance.
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The deleteproject option permits to remove a project from an instance.
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Example :
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Example :
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```bash
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python ./bin/ngspipelines_cli.py deleteproject --project-name MyProject
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python ./bin/ngspipelines_cli.py deleteproject --project-name MyProject
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```
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=Delete an instance =
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# Delete an instance
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This sub command will delete instance repository but NOT project inside instance.
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This sub command will delete instance repository but NOT project inside instance.
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Example :
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Example :
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```bash
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python ./bin/ngspipelines_cli.py deleteinstance --project-name myinstance
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python ./bin/ngspipelines_cli.py deleteinstance --project-name myinstance
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```
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=Launch web server=
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# Launch web server
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Once you have loaded the data in you project you can give access to the user interface by launching the instance using the runinstance option. This will start the corresponding web-server.
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Once you have loaded the data in you project you can give access to the user interface by launching the instance using the runinstance option. This will start the corresponding web-server.
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Example :
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Example :
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```bash
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python ./bin/ngspipelines_cli.py runinstance --instance-name myinstance
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python ./bin/ngspipelines_cli.py runinstance --instance-name myinstance
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```
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To stop the web-server use :
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To stop the web-server use :
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Example :
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Example :
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```bash
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python ./bin/ngspipelines_cli.py runinstance --instance-name myinstance --command stop
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python ./bin/ngspipelines_cli.py runinstance --instance-name myinstance --command stop
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```
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=Web-server connection=
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# Web-server connection
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Once the web-server is started you will be able to access it using the URL.
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Once the web-server is started you will be able to access it using the URL.
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The URL has to include the port separated by ':' .
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The URL has to include the port separated by ':' .
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Example :
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Example :
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```bash
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http://ngspipelines.toulouse.inra.fr:9000/
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http://ngspipelines.toulouse.inra.fr:9000/
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``` |
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\ No newline at end of file |