Open mgalland opened 3 years ago
anfederico
commented
3 years ago My first thought would be an issue with Pandoc. Is it available / updated? pandoc -v. I don't believe it's pre-bundled into the Docker image so you might need to activate Pandoc in your cloud environment.
mgalland
commented
3 years ago Here's what I have pre-installed on my system:
pandoc 1.12.3.1
Compiled with texmath 0.6.6, highlighting-kate 0.5.6.
Syntax highlighting is supported for the following languages:
actionscript, ada, apache, asn1, asp, awk, bash, bibtex, boo, c, changelog,
clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css, curry, d,
diff, djangotemplate, doxygen, doxygenlua, dtd, eiffel, email, erlang,
fortran, fsharp, gnuassembler, go, haskell, haxe, html, ini, java, javadoc,
javascript, json, jsp, julia, latex, lex, literatecurry, literatehaskell,
lua, makefile, mandoc, markdown, matlab, maxima, metafont, mips, modelines,
modula2, modula3, monobasic, nasm, noweb, objectivec, objectivecpp, ocaml,
octave, pascal, perl, php, pike, postscript, prolog, python, r,
relaxngcompact, restructuredtext, rhtml, roff, ruby, rust, scala, scheme,
sci, sed, sgml, sql, sqlmysql, sqlpostgresql, tcl, texinfo, verilog, vhdl,
xml, xorg, xslt, xul, yacc, yamlIs that version of pandoc too old? I guess including it in the Dockerfile could be a good solution then.
For one Docker image that I use with R to make PDF out of R Markdown files, I copy-pasted these lines from the rocker/verse image. Maybe that helps Thank you Marc
# Version-stable CTAN repo from the tlnet archive at texlive.info, used in the
# TinyTeX installation: chosen as the frozen snapshot of the TeXLive release
# shipped for the base Debian image of a given rocker/r-ver tag.
# Debian buster => TeXLive 2018, frozen release snapshot 2019/02/27
ARG CTAN_REPO=${CTAN_REPO:-https://www.texlive.info/tlnet-archive/2019/02/27/tlnet}
ENV CTAN_REPO=${CTAN_REPO}
ENV PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/
## Add LaTeX, articles and bookdown support
RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
&& dpkg -i texlive-local.deb \
&& rm texlive-local.deb \
&& apt-get update \
&& apt-get install -y --no-install-recommends \
default-jdk \
fonts-roboto \
ghostscript \
less \
libbz2-dev \
libicu-dev \
liblzma-dev \
libhunspell-dev \
libjpeg-dev \
libmagick++-dev \
libopenmpi-dev \
librdf0-dev \
libtiff-dev \
libv8-dev \
libzmq3-dev \
qpdf \
ssh \
texinfo \
vim \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/ \
## Use tinytex for LaTeX installation
&& install2.r --error tinytex \
## Admin-based install of TinyTeX:
&& wget -qO- \
"https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \
sh -s - --admin --no-path \
&& mv ~/.TinyTeX /opt/TinyTeX \
&& if /opt/TinyTeX/bin/*/tex -v | grep -q 'TeX Live 2018'; then \
## Patch the Perl modules in the frozen TeX Live 2018 snapshot with the newer
## version available for the installer in tlnet/tlpkg/TeXLive, to include the
## fix described in https://github.com/yihui/tinytex/issues/77#issuecomment-466584510
## as discussed in https://www.preining.info/blog/2019/09/tex-services-at-texlive-info/#comments
wget -P /tmp/ ${CTAN_REPO}/install-tl-unx.tar.gz \
&& tar -xzf /tmp/install-tl-unx.tar.gz -C /tmp/ \
&& cp -Tr /tmp/install-tl-*/tlpkg/TeXLive /opt/TinyTeX/tlpkg/TeXLive \
&& rm -r /tmp/install-tl-*; \
fi \
&& /opt/TinyTeX/bin/*/tlmgr path add \
&& tlmgr install ae inconsolata listings metafont mfware parskip pdfcrop tex \
&& tlmgr path add \
&& Rscript -e "tinytex::r_texmf()" \
&& chown -R root:staff /opt/TinyTeX \
&& chmod -R g+w /opt/TinyTeX \
&& chmod -R g+wx /opt/TinyTeX/bin \
&& echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
&& install2.r --error PKI \
## And some nice R packages for publishing-related stuff
&& install2.r --error --deps TRUE \
bookdown rticles rmdshower rJava
Dear creators of nf-gwas-pipeline, First a praise: I was looking for such a long time for a nice and well documented GWAS pipeline. I must say I've tried quite a few and there was always an issue somewhere (installation or when making a Docker image). So far I find it super convenient and super easy to install thanks to Docker in my case.
I have an issue with the report step of the pipeline when using it with Docker.
I am trying the pipeline on the test dataset for now using Docker. Here is what I execute:
Command
Output
The last step (report) writes this (long) error message:
My guess is that it has to do with the knitting of the Rmd since it goes all the way to the end. Could be some Tex-related dependencies? If you have a guess, I'd be happy to tryout the fixed version. Thanks again for your pipeline + nice documentation + JOSS paper. Cheers Marc
Config
Config (cloud machine from Digital Ocean):