From a1f6c16ce6a4743ea9c861efc6a321e109d5cf9d Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Jun 2021 11:18:50 -0400 Subject: [PATCH 1/5] upgrades to bids validator v1.7.2 (from 1.2.5) --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e68bf81..e4cb374 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,7 @@ MAINTAINER ENV HEUDICONVTAG v0.5.4 #bids validator version: -ENV BIDSTAG 1.2.5 +ENV BIDSTAG v1.7.2 #pydeface version: ENV PYDEFACETAG v1.1.0 From 52198b4f3e6681aeb4c564c54f1205be0b15d297 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Jun 2021 11:37:53 -0400 Subject: [PATCH 2/5] update nodejs from v8 to v16 was failing test --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e4cb374..9d7f712 100644 --- a/Dockerfile +++ b/Dockerfile @@ -128,7 +128,7 @@ COPY . /opt/tar2bids RUN apt-get update && \ apt-get install -y curl git && \ - curl -sL https://deb.nodesource.com/setup_8.x | bash - && \ + curl -sL https://deb.nodesource.com/setup_16.x | bash - && \ apt-get remove -y curl && \ apt-get install -y nodejs && \ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* From 97494dd71a1f58d60e733ca882fcadf1175a22e1 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Jun 2021 12:48:08 -0400 Subject: [PATCH 3/5] Update Dockerfile --- Dockerfile | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9d7f712..8a53553 100644 --- a/Dockerfile +++ b/Dockerfile @@ -127,11 +127,7 @@ COPY . /opt/tar2bids RUN apt-get update && \ - apt-get install -y curl git && \ - curl -sL https://deb.nodesource.com/setup_16.x | bash - && \ - apt-get remove -y curl && \ - apt-get install -y nodejs && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + apt-get install -y git nodejs RUN git clone https://github.com/bids-standard/bids-validator /opt/bids-validator && \ cd /opt/bids-validator && \ From 0b5d8771f3f67bf562e883b259c705dea4cf54db Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Jun 2021 12:53:27 -0400 Subject: [PATCH 4/5] install npm --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8a53553..e75f6c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -127,7 +127,7 @@ COPY . /opt/tar2bids RUN apt-get update && \ - apt-get install -y git nodejs + apt-get install -y git nodejs && apt-get install -y npm RUN git clone https://github.com/bids-standard/bids-validator /opt/bids-validator && \ cd /opt/bids-validator && \ From 88ccb30082b41f56dac5a292b3ad1215c251704c Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Jun 2021 13:11:50 -0400 Subject: [PATCH 5/5] follow recommended instructions for bids validator --- Dockerfile | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/Dockerfile b/Dockerfile index e75f6c4..e8b3e1e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,9 +4,6 @@ MAINTAINER #heudiconv version: ENV HEUDICONVTAG v0.5.4 -#bids validator version: -ENV BIDSTAG v1.7.2 - #pydeface version: ENV PYDEFACETAG v1.1.0 @@ -123,16 +120,9 @@ RUN mkdir -p /opt/tar2bids COPY . /opt/tar2bids ## Install bids-validator - - - RUN apt-get update && \ - apt-get install -y git nodejs && apt-get install -y npm - -RUN git clone https://github.com/bids-standard/bids-validator /opt/bids-validator && \ - cd /opt/bids-validator && \ - git checkout $BIDSTAG && \ - npm install -g /opt/bids-validator/bids-validator + apt-get install -y git nodejs && apt-get install -y npm && \ + npm install --global npm@^7 && npm install -g bids-validator #install gnu parallel RUN apt-get update && apt-get install -y parallel