Potential packages to pass the sanity check

[JesperBrink]

Right now we can build the kallisto package. What we want next is to find another project with a CMakeList and make sure that our program can build that project too, while still being able to build kallisto.

[JesperBrink]

Here are some ideas for packages with a CMakeLists file that we could try to build, with comments to why they might be interessting:

htstream

• Has 2 packages we can't handle yet (xz, boost)
• Needs both the c and the cxx compiler. (Right now we only handle the cxx compiler)

sailfish

• Has 5 packages we can't handle yet (boost, tbb, unzip, perl, icu)

dcmtk

• Has 5 packages we havn't seen yet (openssl, libpng, libtiff, jpeg, libxml2)

kmerinshort

• Very simple, it only needs zlib
• Could give us another way to detect zlib
• It uses md5 instead of sha. This could help us generalize our code away from only using sha.

clever-toolkit

• Has 6 packages we can't handle yet (boost, python, bedtools, samtools, bcftools, matplotlib)
• One of the dependencies (bedtools) needs to be version 2.26 or newer. (A way to learn how to handle these type of situations)

[Hogfeldt]

After our weekly meeting with Dan we decided to expand with the following packages in descending order:

• kmerinshort
• sailfish
• htstream

[JesperBrink]

After working with the kmerinshort package, we realised that it wasn't that 'simple' at all. There where a lot of packages not included in the recipe, and we could not build the package even when we used their recipe. We therefore chose to focus on the next package on the list: sailfish.

[JesperBrink]

We will also skip sailfish, since this is a linux only package. We could maybe come back to this package later on, since this is an interesting feature to be able to handle.

[JesperBrink]

We can successfully build htstream with Bioconda utils on its own recipe. We will therefore chose this as the next package to implement.

[Hogfeldt]

We have created a project board here on Github. This issue will be used to making suggestions on which packages we wan't to try and get through the sanity check. When a package is approved we create a card on the project board and when a card moves from To Do to In Progress, an issue should be created.

[JesperBrink]

The following packages can build with bioconda-utils:

blasr_libcpp:

• Has packages we havn't seen
• Requires minimum version numbers

qfilt:

• Very simple (only needs cmake and cxx compiler)
• Still interesting to see if we can build it, which we should be able to do at this point

libdivsufsort:

• Very simple
• Uses a c compiler instead of cxx, which we currently only support

[JesperBrink]

The following packages can build with bioconda-utils:

tn93:

• Uses both the c and the cxx compiler
• Otherwise every simple

bpp-popgen:

• The meta.yaml file has one package we don't know
• The build.sh does more things than ours. Could be interesting to see if our build.sh is enough or it should be updated to handle these type cases too.

[JesperBrink]

The blasr_libcpp turned out not to contain a CMakeLists.txt file and should therefore not be tried to build right now