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c-guzman / cipher-workflow-platform

A data processing platform for ChIP-seq, RNA-seq, MNase-seq, DNase-seq, ATAC-seq and GRO-seq datasets. Please ignore information on cipher.readthedocs.io, it is currently out of date. Follow information in README.
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Error when we prepare singularity machine #4

Closed bioinfo-dirty-jobs closed 7 years ago

bioinfo-dirty-jobs commented 7 years ago

Here you can see the error I obtain when I try to bootstrap the machine with last git

Creating file system within image
Image is done: cipher.img
[root@localhost cipher-workflow-platform]#  singularity bootstrap cipher.img Singularity
Sanitizing environment
Building from bootstrap definition recipe
Adding base Singularity environment to container
Docker image path: index.docker.io/library/ubuntu:16.04
ERROR Improperly formed manifest, layers or fsLayers must be present
[root@localhost cipher-workflow-platform]# git log
commit e4280c935a7dc37b3769daf858f2fb1ce2d8c4ce
Author: Carlos Guzman <carlos@Carloss-MacBook-Pro.local>
Date:   Mon Sep 11 11:02:11 2017 -0700

    Added jellyfish to Singularity image

commit 042e25f220417823b7efedb78a2af28ef51de727
Author: Carlos Guzman <carlos@Carloss-MacBook-Pro.local>
Date:   Mon Sep 11 08:41:15 2017 -0700
c-guzman commented 7 years ago

Docker updated their manifest last night which broke Singularity. The devs have fixed this and will push out a fix soon, so I'll let you know when you can update Singularity and that should fix the problem.

Sorry about that!

c-guzman commented 7 years ago

Singularity PR has been updated, please update your Singularity! This will fix the problem!

bioinfo-dirty-jobs commented 7 years ago

Sorry could you help me how to update? I try to install also the last development installation but not work..

rm -rf /usr/local/libexec/singularity
git clone https://github.com/singularityware/singularity.git
cd singularity
./autogen.sh
./configure --prefix=/usr/local
make
sudo make install

[root@localhost cipher-workflow-platform]# singularity bootstrap cipher.img Singularity
Sanitizing environment
Building from bootstrap definition recipe
Adding base Singularity environment to container
Docker image path: index.docker.io/library/ubuntu:16.04
ERROR Improperly formed manifest, layers or fsLayers must be present
[root@localhost cipher-workflow-platform]#
bioinfo-dirty-jobs commented 7 years ago

I resolve using this:

git clone -b development https://github.com/singularityware/singularity.git