VirtualBox list

[satra]

@mjtravers - replacing issue #12 - just check off all the things you already have.

Core VM

• [x] memory 2G (needs to be tested)
• [x] cores 2
• [x] xenial LTS desktop
  • [x] neurodebian sources
• [x] autologin full-screen
• [x] latest guest additions

general (see each section for additional local installs (listed under install)

• [x] git
• [x] git-annex-standalone
• [x] editors: vim emacs pico nano gedit
• [x] docker 18.03.1-ce
• [x] Singularity 2.5.1-dist
• [x] build-essential
• [x] wget curl

FAIR Data - BIDS datasets

• instructions from here: https://github.com/albertcrowley/nidm-training
  • install
  • [x] graphviz
• miniconda (environment: section1)
  • conda
  • [x] python=3 pytest graphviz pandas rdflib requests fuzzywuzzy pygithub python-levenshtein
  • pip
  • [x] owlready2 pybids duecredit https://github.com/incf-nidash/PyNIDM/archive/a90b3f47dbdafb9504f13a3a8d85fdff931cc45c.zip
  • [x] git clone https://github.com/incf-nidash/PyNIDM.git

Computational basis

• [x] Datalad @yarikoptic - let matt know when this is released
• pip:
  • [x] https://github.com/datalad/datalad-container/archive/master.zip
  • [x] https://github.com/datalad/datalad-neuroimaging/archive/master.zip

Neuroimaging Workflows

• containers
  • [x] neurodocker (docker pull kaczmarj/neurodocker:master) - will ask @kaczmarj to cut a new release
• [x] fsl heudiconv (build using instructions below)
• [x] Reprozip/Reprounzip (installed via miniconda above into environment: section3)

Statistics for reproducibility

• [x] requirements installed into separate environment (environment: section4)

Others

• [ ] Vagrantfile
• [ ] All the neurodocker scripts for containers
• [ ] niceman into containers?? (@yarikoptic @mjtravers - should this be done?)
• [ ] instructions for building the singularity containers (testing these now - will add soon)

[jbpoline]

@mjtravers Awesome - thanks ! @cmtgreenwood : let us know if that is fine - best would be to try on the VM - will try on my side

[cmtgreenwood]

managed to launch Rstudio successfully inside the updated VM. Looking for where the scripts are located in the VM. Will be back on this only tomorrow morning

[djarecka]

@cmtgreenwood for the scripts you have to clone this github repository. They are not part of the VM (but during training it will be cloned during git part)

after you clone the repository, your scripts are in ohbm2018-training/section4/section41

[cmtgreenwood]

Good news and bad news:

• successful clone onto my virtual box of ohbm-training
• rstudio starts fine
• sections of the code (run separately) inside the Rmd file run fine, with one small change needed to the code (the path to the dataset needs modification)

However, knitr fails. It requested updates of two packages (catools, bitops) and apparently installed them OK, but then I received this message:

Error in yaml::yaml.load(string, ...) : Parser error: while parsing a block mapping at line 1, column 1 did not find expected key at line 1, column 45 Calls: ... parse_yaml_front_matter -> yaml_load_utf8 -> -> .Call Execution halted

This is not a major problem, since knitr just compiles everything into one file. Even without this compilation, it is possible to see the results.

[jbpoline]

Ok - so - room for improvement but in the worse case we should survive :) looks like a knitr "front" file is missing or something ... try re-installing knitr in the VM may be ?

[mjtravers]

@cmtgreenwood If you send me the script that is having the issue, I can see if I can sort out a fix.