Caching assorted protein analysis tools

[peterjc]

See #88 about formalising the sorting for the urls.tsv file.

I deliberately sorted the file before adding these entries used in some of my tool wrappers defined in https://github.com/peterjc/pico_galaxy

[peterjc]

TravisCI failed on some of the sort changes, apparently the checksums have changed for http://www.imagemagick.org/download/ImageMagick.tar.gz and https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.28.2.tar.gz

[peterjc]

Quoting from the TravisCI ouput,

{'upstream_first': 'True', 'url': 'http://www.imagemagick.org/download/ImageMagick.tar.gz', 'sha256sum': '5617e14d624be393209d77674b935165bddc797e65661774f81785f6c05ca0e9', 'platform': 'src', 'ext': '.tar.gz', 'version': '6.9.3', 'arch': 'all', 'id': '+ImageMagick'}
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 12.1M  100 12.1M    0     0  12.4M      0 --:--:-- --:--:-- --:--:-- 14.1M
INFO:root:ImageMagick_6.9.3_src_all.tar.gz downloaded successfully
INFO:root:File hash 59f92ba318a976ebf5148f26efd6bb59a636e823e7ec5765c841fe1c160da285
ERROR:root:File has bad hash! 59f92ba318a976ebf5148f26efd6bb59a636e823e7ec5765c841fe1c160da285 != 5617e14d624be393209d77674b935165bddc797e65661774f81785f6c05ca0e9 in ImageMagick_6.9.3_src_all.tar.gz
Traceback (most recent call last):
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 859, in emit
    msg = self.format(record)
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 732, in format
    return fmt.format(record)
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 471, in format
    record.message = record.getMessage()
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 335, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Logged from file galaxy-cachefile-external-validator, line 28

and:

{'upstream_first': 'True', 'url': 'https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.28.2.tar.gz', 'sha256sum': '96b3c01e2c6709ee8fb4c43583b22ea0a6f32624b73a9c05d74cac4c443ad342', 'platform': 'src', 'ext': '.tar.gz', 'version': '3.28.2', 'arch': 'all', 'id': '+limma'}
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  6777  100  6777    0     0   124k      0 --:--:-- --:--:-- --:--:--  194k
INFO:root:limma_3.28.2_src_all.tar.gz downloaded successfully
INFO:root:File hash 45f5d7bf044eae67bf5e3b33d4fdea6013d243715d56735f476ca21274b72350
ERROR:root:File has bad hash! 45f5d7bf044eae67bf5e3b33d4fdea6013d243715d56735f476ca21274b72350 != 96b3c01e2c6709ee8fb4c43583b22ea0a6f32624b73a9c05d74cac4c443ad342 in limma_3.28.2_src_all.tar.gz
Traceback (most recent call last):
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 859, in emit
    msg = self.format(record)
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 732, in format
    return fmt.format(record)
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 471, in format
    record.message = record.getMessage()
  File "/opt/python/2.7.9/lib/python2.7/logging/__init__.py", line 335, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Logged from file galaxy-cachefile-external-validator, line 28

There is clearly a minor Python error in the logging call, which I would be happy to fix, but where is galaxy-cachefile-external-validator defined? I can see it gets invoked via https://github.com/galaxyproject/cargo-port/blob/master/.ci/build.sh and https://github.com/galaxyproject/cargo-port/blob/master/.ci/check.sh

[peterjc]

Found the script bin/galaxy-cachefile-external-validator aka bin/travis.py, it seems GitHub's search may overlook symlinks?

https://github.com/galaxyproject/cargo-port/blob/master/bin/travis.py

[peterjc]

@erasche do you want me to rebase this doing the dedup.py sort instead? That will reduce the changes.

[peterjc]

Please look at #91 for the sorting issues, after which I will rebase with just the new URLs.