Create .travis.yml …

Travis-CI test should run from now on

greatfireball committed May 12, 2016

Added testing under osx and linux to travis.yml …

I am using the new feature to test under different operation systems.

Therefore, we should be able to guarantee that the SeqChunker works under Linux and MacOSX

greatfireball committed May 12, 2016

Skipping installation step …

According to https://docs.travis-ci.com/user/customizing-the-build/#Customizing-the-Installation-Step the installation step to resolve dependencies can be avoided. In our project that makes sense due to we have no real perl program running

greatfireball committed May 12, 2016

Ignoring build failures under osx …

Due to we are sure about the MacOSX version, I tollerate build failures under osx

greatfireball committed May 12, 2016

Added a bash function to avoid redundancy …

I added a litte bash function to avoid redundancy during testing

greatfireball committed May 12, 2016

Removed first to fasta checks due to they are already performed using… …

… the test_fasta function

greatfireball committed May 12, 2016

Removed deletion of temporary files to start of test script

greatfireball committed May 12, 2016

Avoiding test problems if output files are not existing

greatfireball committed May 12, 2016

Renamed PIPE_FLAG to SPECIAL_FLAG

greatfireball committed May 12, 2016

Set an empty default SPECIAL_FLAG

greatfireball committed May 12, 2016

Added a test against individual files from last run controlled by SPE… …

…CIAL_FLAG

greatfireball committed May 12, 2016

Added the third test based on the bash function

greatfireball committed May 12, 2016

Removed old test #3

greatfireball committed May 12, 2016

Added the fifth test based on the bash function

greatfireball committed May 12, 2016

Removed old test #5

greatfireball committed May 12, 2016

Added the sixth test based on the bash function

greatfireball committed May 12, 2016

Removed old test #6

greatfireball committed May 12, 2016

Added the fourth test based on the bash function plus one preparation… …

… test

greatfireball committed May 12, 2016

Removed old test #4

greatfireball committed May 12, 2016

Added a commentary to show where the test will be started

greatfireball committed May 12, 2016

Renamed test function to test_SeqChunker, corrected the test-names, a… …

…nd moved input file definition down to tests

greatfireball committed May 12, 2016

Added the first FASTQ test based on the bash function

greatfireball committed May 12, 2016

Removed old FASTQ test #1

greatfireball committed May 12, 2016

Added the second FASTQ test based on the bash function

greatfireball committed May 12, 2016

Removed old FASTQ test #2

greatfireball committed May 12, 2016

Added the third FASTQ test based on the bash function

greatfireball committed May 12, 2016

Removed old FASTQ test #3

greatfireball committed May 12, 2016

Added the fourth FASTQ test based on the bash function plus one prepa… …

…rational test

greatfireball committed May 12, 2016

Removed old FASTQ test #4

greatfireball committed May 12, 2016

Added the fifth FASTQ test based on the bash function plus one prepar… …

…ational test

greatfireball committed May 12, 2016

Removed old FASTQ test #5

greatfireball committed May 12, 2016

Cleaning up

greatfireball committed May 12, 2016

Skipping md5 based tests for now

greatfireball committed May 12, 2016

Now cycling through all implementations of SeqChunker

greatfireball committed May 12, 2016

Added TAP directive support and enable TODO directive for SeqChunker-… …

…sed, due to it seems to be broken

greatfireball committed May 12, 2016

New version 0.4 should work on MacOSX as well as Linux

greatfireball committed May 12, 2016

Put declaration of TAP_DIRECTIVE outside the current block

greatfireball committed May 12, 2016

Added a test, if bash >= 4 is present

greatfireball committed May 12, 2016

Fixed a typo in to test, which results in failing test without recogn… …

…izing it

greatfireball committed May 12, 2016

Each test generates individual set of output files …

Changed the way, the combined output will be generated. So each test will
generate its own set of output files. The name of the output files are generated
according to:

	  tmp.TESTNUMBER.*

So the tests if the correct output was generated can now avoid diff, but use the
md5sum of the output instead.

greatfireball committed May 12, 2016

Switch to local variables for function

greatfireball committed May 13, 2016

Added a reference.md5 file for expected MD5 sums for first 14 tests

greatfireball committed May 13, 2016

Added a new function for md5 based tests

greatfireball committed May 13, 2016

Removed old diff based test for expected output by md5 checksum based… …

… approach

greatfireball committed May 13, 2016

Changed to prove harnest to run tests …

This is expected to fail for the original test script, but should work on the new one

greatfireball committed May 13, 2016

Added missing md5 reference sums …

To generate the sums based on the original one, I used the following perl statement:

```
perl -ne '

     unless (/tmp/) { print; next }

     print;

     foreach my $fact (map {$_*14} (1..3))
     {
	$bla=$_;
	$bla=~s/(?<=\.)(\d+)(?=\.)/$1+$fact/eg; print $bla;
     }

' reference.md5
```

greatfireball committed May 13, 2016

Merge pull request #8 from BioInf-Wuerzburg/feature/travis-ci-testing …

Testing at Travis-CI is now available

greatfireball committed May 14, 2016

Removed the allowed failure on MacOSX

greatfireball committed May 14, 2016