Hello
(Please CC me, not subscribed to list)
I have been trying to create a snap package for the `cufflinks` [1]
biofinformatics tools. These are packaged for debian/ubuntu, but the
package is not built for xenial due to issues with boost 1.56-1.59. [2]
I tried building a snap package (see snapcraft.yaml below - just a
simple `stage-packages` build) on yakkety in order to bundle the
relevant dependencies and then install it on xenial, but I ran into the
following issues:
* Trying to run any of the binaries gives the error
failed to create user data directory. errmsg: Permission denied
This is presumably related to #1592696, but in this case $HOME is on
an NFS mount under /mnt. Probably an uncommon case, but this probably
isn't the only such configuration.
* The package contains multiple binaries, and the links in /snap/bin
are named, eg `cufflinks.cuffdiff`, which makes them incompatible with
existing scripts. Additionally, I can't declare `apps:` keys with
underscores in them, so some come out completely misnamed.
Did I miss an option somewhere to better control command naming?
Snap packages are potentially quite useful for scientific tools with odd
sets of dependencies - where confinement is not an issue, but it
provides a much easier way to handle private library versions, etc.
Gordon
[1]: https://github.com/cole-trapnell-lab/cufflinks
[2]: https://launchpad.net/ubuntu/+source/cufflinks
----8<-snapcraft.yaml-8<----
name: cufflinks
version: 2.2.1
summary: Transcript assembler
description: |
Cufflinks assembles transcripts, estimates their abundances, and
tests for
differential expression and regulation in RNA-Seq samples. It
accepts aligned
RNA-Seq reads and assembles the alignments into a parsimonious set of
transcripts. Cufflinks then estimates the relative abundances of these
transcripts based on how many reads support each one, taking into
account biases
in library preparation protocols.
confinement: devmode
apps:
compressgtf:
command: compress_gtf
cuffcompare:
command: cuffcompare
cuffdiff:
command: cuffdiff
cufflinks:
command: cufflinks
cuffmerge:
command: cuffmerge
cuffnorm:
command: cuffnorm
cuffquant:
command: cuffquant
gffread:
command: gffread
gtftosam:
command: gtf_to_sam
parts:
cufflinks:
plugin: nil
stage-packages:
- cufflinks
- libboost-serialization1.61.0
- libboost-system1.61.0
- libboost-thread1.61.0
- libstdc++6
- zlib1g
- libc6
- libgcc1
----8<----
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