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JasonJWilliamsNY / dc_genomics_docker

Container development for Data Carpentry Genomics lessons
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Add curl and curl-dev to install #6

Closed naupaka closed 5 years ago

naupaka commented 5 years ago

I having issues running through the shell lessons -- perhaps because curl-dev need to be installed on the image?

naupaka commented 5 years ago

e.g.

dcuser@e315149a7068:/docker-persistant/data/untrimmed_data$ curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/004/SRR2589044/SRR2589044_1.fastq.gz
curl: (48) An unknown option was passed in to libcurl
naupaka commented 5 years ago

From: https://datacarpentry.org/wrangling-genomics/02-quality-control/index.html

naupaka commented 5 years ago

wget works as a substitute

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/004/SRR2589044/SRR2589044_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/004/SRR2589044/SRR2589044_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584866/SRR2584866_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584866/SRR2584866_2.fastq.gz
naupaka commented 5 years ago

Some discussion here: https://stackoverflow.com/questions/11678085/curl-48-an-unknown-option-was-passed-in-to-libcurl

naupaka commented 5 years ago

Another issue later, same problem:

dcuser@e315149a7068:/docker-persistant/data/ref_genome$ curl -L -o ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
curl: (48) An unknown option was passed in to libcurl
dcuser@e315149a7068:/docker-persistant/data/ref_genome$ wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
dcuser@e315149a7068:/docker-persistant/data/ref_genome$ mv GCA_000017985.1_ASM1798v1_genomic.fna.gz ecoli_rel606.fasta.gz
JasonJWilliamsNY commented 5 years ago

This seems to work when i do it...

$ curl -O ftp://ftp.ensemblgenomes.org/pub/release-37/bacteria/species_EnsemblBacteria.txt % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 8156k 100 8156k 0 0 2550k 0 0:00:03 0:00:03 --:--:-- 2550k

will reopen if it reappears later