... | ... | @@ -56,16 +56,12 @@ Example : |
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--assembly-annot file=workflows/rnaseqdenovo/data/best_annotation_file.gff3 software-name=blastall software-parameters="-e 10e-10" software-version="2.2.26" comments="Best annotations against swissprot" is-best
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```
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'''At least one bam is required, and the bam file name must correspond to the library name.'''
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At least one bam is required, and the bam file name must correspond to the library name. If you've done your own counting expression you can provide the matrix file with contigs names, see option --count-matrix for more details.
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If you've done your own counting expression you can provide the matrix file with contigs names, see option --count-matrix for more details.
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## General options
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==General options==
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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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''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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### --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. 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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* library-name* : [string] the internal library name, must be uniq
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... | ... | @@ -74,11 +70,11 @@ List of available attribute (with * mandatory attribute): |
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* tissue : [string] tissue
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* dev_stage : [string] developpement stage
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* type* : [string] library type , available options :
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** se : single end
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** pe : paired end
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** ose : oriented single end
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** ope : oriented paired end
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** mp : mate pair
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* se : single end
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* pe : paired end
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* ose : oriented single end
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* ope : oriented paired end
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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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* remark : [string] any comment
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* sequencer : [string] sequencer type
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... | ... | @@ -89,12 +85,12 @@ 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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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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sequencer=HiSeq2000 files=workflows/rnaseqdenovo/data/brain_400.1.fastq.gz,workflows/rnaseqdenovo/data/brain_400.2.fastq.gz
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===--assembly [mandatory] ===
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```
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### --assembly [mandatory]
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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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... | ... | @@ -103,10 +99,12 @@ The assembly option is mandatory. The possible attributes are : |
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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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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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```
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===--assembly-annot [mandatory] ===
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### --assembly-annot [mandatory]
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The annotation option attributes are :
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* file* : contigs annotation file in GFF3 [http://gmod.org/wiki/GFF3] with some specials attributes.
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... | ... | @@ -117,24 +115,22 @@ The annotation option attributes are : |
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* is-best : [bool] to define if the file corresponds to the best annotation file [true|false]
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If you have computed several annotations you have to use the annotation option several times.
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Example :
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Example :
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```bash
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--assembly-annot file=workflows/rnaseqdenovo/data/best_annotation_file.gff3 software-name=blastall software-parameters="-e 10e-10" \
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software-version="2.2.26" comments="Annotations against swissprot"
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```
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If you do not provide a best annotation file (one contig per line in this file, see [[annotation file]] format) then you can specify which annotation source (source column of the GFF3 file) has to be used by the pipeline in order to compute the contigs best annotation.
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Example :
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Example :
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```bash
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--assembly-annot file=workflows/rnaseqdenovo/data/annotation_swissprot.gff3 software-name=blastall software-parameters="-e 10e-10" \
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software-version="2.2.26" comments="Annotations against swissprot" --best-annotation-source swissprot
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More info about [[annotation file]]
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```
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===--alignment [mandatory]===
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### --alignment [mandatory]
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To provide alignment file (bam) and associate analysis, the user must use the option --alignment.
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The pipeline will sort and index the bam files. If the --count-matrix option is not provided, the expression measurment is performed.
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Here is the list of attributes of this options :
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... | ... | @@ -145,38 +141,38 @@ Here is the list of attributes of this options : |
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* comments : [string] any comments on this analysis
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Example :
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```bash
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--alignment file=/path/to/lib1.bam file=/path/to/lib2.bam software-name=bwa software-parameters=aln/samse software-version="0.7.2-r351" comments="Library alignment against contigs"
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```
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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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Example :
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```bash
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--go go.txt
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```
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More info about [[ go file ]]
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===--keyword===
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### --keyword
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This file contains for each contig one line with keywords (separated by tabulation).
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Example:
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```bash
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--keyword keywords.txt
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```
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More info about [[keyword file]]
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===--count-matrix===
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### --count-matrix
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The pipeline performs the expression measurement (see above for more information). You can skip this step if you've built your own matrix and provide it using the --count-matrix option.
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Contigs are in line and library count in column. First line must contain the libraries names.
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Example :
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Example :
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```bash
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--count-matrix matrix.txt
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```
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More info about [[expression measurement and matrix format]]
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===--variant===
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### --variant
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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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If the VCF file has been produced using GATK [http://www.broadinstitute.org/gatk/], the allelic count per library will be extracted from the VCF file.
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... | ... | @@ -188,10 +184,12 @@ Here is the list of attributes for this options : |
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* software-version : [string] detection software version
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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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```
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===--variant-annot===
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### --variant-annot
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Variation annotation information has to be provided in gff3 format and includes some specific attributes.
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This option was design to store SNP annotations. Its usually produced by alignment versus a closely genome. The alignment position on the genome enables to extract :
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... | ... | @@ -210,44 +208,44 @@ Here is the list of attributes of this options : |
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* is-best : [bool] defines if the file correspond to the best annotation file [true|false]
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If you have several annotation file you have to use this option several times.
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Example :
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Example :
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```bash
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--variant-annot file=workflows/rnaseqdenovo/data/variant_best_annotation.gff software-name=tSNPannot software-parameters="-p blastall -e 10-e10 --species Danio rerio" \
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software-version="1" comments="Best annotation of snp" is-best=true
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```
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As for contig annotations, if you don't have a best annotation file you can use the option --variant-best-annotation-source.
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Example :
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Example :
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```bash
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--variant-annot file=workflows/rnaseqdenovo/data/variant_annotation.gff software-name=tSNPannot software-parameters="-p blastall -e 10-e10 --species Danio rerio" \
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software-version="1" comments="Annotation of snp" --variant-best-annotation-source "tSNPannot"
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```
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More info about [[variant annotation file]]
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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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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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=Launch web server=
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```
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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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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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```
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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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=Web-server connection=
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```
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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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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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|
``` |
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\ No newline at end of file |