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User: cdastmalchi

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Posts by cdastmalchi

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Can't install DESeq2 via Docker container because of dependency issues
... Also, when I try to run your container above (but with DESeq2 and its dependencies) and then run it interactively, I get: ERROR: You must set a unique PASSWORD (not 'rstudio') first! e.g. run with: docker run -e PASSWORD= -p 8787:8787 rocker/rstudio ...
written 12 weeks ago by cdastmalchi • 0
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Comment: C: Can't install DESeq2 via Docker container because of dependency issues
... Thanks! Is it feasible to combine the `bioconductor/release_base2` image with like an Ubuntu image so that I can install python packages as well (as I'll be running this on a python-based bioinformatics pipeline)? When I tried a multi-image Dockerfile, it couldn't find R (see update). ...
written 12 weeks ago by cdastmalchi • 0
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Can't install DESeq2 via Docker container because of dependency issues
... I have been trying to install DESeq2 via a Docker container, running it interactively, and then starting an R session where I can manually install the package. Here is my Dockerfile, which pulls down R version 3.4.1 and installs additional packages on top of it. FROM r-base:3.4.1 W ...
gene R deseq2 docker rna-seq written 12 weeks ago by cdastmalchi • 0 • updated 12 weeks ago by sviatoslav.kendall • 770
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Comment: C: I couldn't install DEseq2?
... `libxml2-dev` is among the packages I install in my Dockerfile. I'll maybe just post this as a new question like you suggested. ...
written 12 weeks ago by cdastmalchi • 0
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Comment: A: I couldn't install DEseq2?
... I'm having this same error when trying to install DESeq2 for R Version 3.6.1, even after adding `sudo apt-get install libxml2` , `sudo apt-get install libxml2-dev`. I'm trying to install deseq2 via a Docker container, for which my Dockerfile looks like: FROM r-base:3.6.1 WORKDIR /home ...
written 3 months ago by cdastmalchi • 0
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Comment: C: Pindel installation failing due to htslib
... Thank you. I have already tried using other directories in the script besides `/usr/bin` for downloading and compiling, however I still get the same error. And the whole point of using a Docker container is to bypass any "manual" steps; I'm trying to use this Pindel program as part of a bioinformati ...
written 4 months ago by cdastmalchi • 0
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Pindel installation failing due to htslib
... I have made the following Dockerfile to install pindel: # Use Python base image from DockerHub FROM python:2.7 RUN apt-get update && apt-get install -y \ bzip2 \ wget \ make \ ncurses-dev \ zlib1g-dev \ g++ \ python-pip \ git ...
htslib docker pindel written 4 months ago by cdastmalchi • 0 • updated 6 weeks ago by steve • 2.5k

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