Is there a database available to query for the TCGA bam files?

Hi, Please explain the use of $self in the Value field of a job input spec. I don't know when and how I can use it. For example, say the ID of my input parameter is called 'quality'. In the JavaScript expression I want to enter in the Value field, it seems I must refer to the parameter as $job.inputs.quality, but I thought I could also do $self.quality. In the documentation at http://docs.cancergenomicscloud.org/docs/dynamic-expressions-in-tool-descriptions#section-the-self-object, it says: """ In the command line bindings for the tool inputs, $self is set to the value of the input. In other words, in this context $self is just $job.inputs.<input_id>. """ According to that documentation, I should be able to use an expression such as "$self || 5" to create a default value of 5. But when doing so, I get this error when trying to run my tool: """ Error This task ran into a problem during execution and did not finish. Failed to start trimgalore. Failed to build command line. Failed to build command line. Failed evaluating expression $self || 20. org.mozilla.javascript.EcmaError: ReferenceError: "$self" is not defined. (script#1). """ So why does it say that $self is not defined?

I am attempting to access project output files through the CGC API. I am using the sevenbridges python package. I have run the code provided on the documentation for accessing projects with initialization via environment variables (https://pypi.python.org/pypi/sevenbridges-python). However, an Unauthorized error is returned. I have double checked and the authentication token I am using is correct. What would be the reason for this?

SVS files are availble through the website: https://portal.gdc.cancer.gov/cases/9fe336a8-08a7-4fe7-bf45-afd6a8eb9c75 They are also available on the data portal as of May 21 2018: (same page, click on Files, it leads to data portal. You can see svs files for this case) However issue an API call to: https://cgc-datasets-api.sbgenomics.com/datasets/v0/tcga/cases/9FE336A8-08A7-4FE7-BF45-AFD6A8EB9C75/files No svs files are available.

H! I have been creating workflow which consists three main steps ( SAMtools View, SAMtools fadix and SAMtools Mpileup). Firstly, with the SAMtools View I filtered the input bam-file based on a bed-file that contains special regions of the third and fifteenth chromosomes. The input bam-file already aligned and sorted I took from the database. The bed-file was download from my computer and the firs line looks like this (3 193593144 193697811). After that the SAMtools Mpileup took file that contain only necessary chromosomes and the file with the indexed reference (as a reference, I used ucsc.hg19.fasta from the database). At the end of the workflow, I expect to see vcf-file with that contains information about the reference and alternative nucleotide of the third and fifteenth chromosomes. Unfortunately, I get the described file, but there are N in place of the reference allele. Please help me understand what is wrong with my reference file

Hi, I'm using STAR genome generate and STAR from public apps (both 2.7.0e) to align a human RNA-seq data (uploaded privately) and I'm using GRCh38.primary_assembly.genome.fa and gencode.v32.annotation.gtf as the reference genome and gene annotation file for genome indices generation. I keep getting this error: Command mkdir genomeDir && STAR --runMode genomeGenerate --genomeDir ./genomeDir --runThreadN 20 --genomeChrBinNbits 16 --limitGenomeGenerateRAM 60000000000 --genomeFastaFiles /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/gencode.v32.annotation.gtf && tar -vcf GRCh38.primary_assembly.genome.gencode.v32.annotation.star-2.7.0e-index-archive.tar ./genomeDir && mv Log.out Log.out.log failed with exit code 137. Can someone tell me how to solve this? Thank you!

Hi, I'm trying to download a SGDP file via wget and the download link. I get error 403. Could you please explain the nature of the error? [[email protected]02 sgdp]$ wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva&x-env=cgc&x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390&x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp&response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz&response-content-type=application%2Foctet-stream&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20220323T140118Z&X-Amz-SignedHeaders=host&X-Amz-Expires=172799&X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5 [2] 9275 [3] 9276 [4] 9277 [5] 9279 [6] 9280 -bash: x-env=cgc: co mmand not found [7] 9281 -bash: x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390: command not found [8] 9282 -bash: x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp: command not found -bash: response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz: command not found [9] 9283 -bash: response-content-type=application%2Foctet-stream: command not found -bash: X-Amz-Algorithm=AWS4-HMAC-SHA256: command not found [10] 9284 [11] 9285 -bash: X-Amz-Date=20220323T140118Z: command not found -bash: X-Amz-SignedHeaders=host: command not found [12] 9286 -bash: X-Amz-Expires=172799: command not found -bash: X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request: command not found --2022-03-23 17:41:00-- https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva -bash: X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5: command not found [3] Exit 127 x-env=cgc [4] Exit 127 x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390 [5] Exit 127 x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp [6] Exit 127 response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz [7] Exit 127 response-content-type=application%2Foctet-stream [8] Exit 127 X-Amz-Algorithm=AWS4-HMAC-SHA256 [9] Exit 127 X-Amz-Date=20220323T140118Z [10] Exit 127 X-Amz-SignedHeaders=host [11] Exit 127 X-Amz-Expires=172799 [12]- Exit 127 X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request [[email protected] sgdp]$ Resolving sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com... 52.217.94.241 Connecting to sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com|52.217.94.241|:443... connected. HTTP request sent, awaiting response... 403 Forbidden 2022-03-23 17:41:01 ERROR 403: Forbidden. [2]- Exit 8 wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva