[BULK] Bioconductor 3.8

[dpryan79]

• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

This is the first PR for Bioconductor 3.8 building. In addition to adding all of the packages, it also does the following:

Changes to config.yml:

• Replaced conda-forge with conda-forge/label/gcc7
• Added bioconda/label/gcc7 ahead of bioconda

These are so we don't need to rebuild all of the bioconductor stuff yet again once the compiler migrations are done. Note that everything in the bulk branch will be uploaded with a gcc7 label attached to it. I'm keeping bioconda in the channel list so we don't have to rebuild everything (I assume that day will soon come...).

Changes to .circleci/config.yml:

@@ -28,6 +28,17 @@ variables:
       LANG: en_US.UTF-8
   linux: &linux
     machine: true
+  macos_bulk: &macos_bulk
+    macos:
+      xcode: "8.3.3"
+    environment:
+      LC_ALL: en_US.UTF-8
+      LANG: en_US.UTF-8
+      BIOCONDA_LABEL: gcc7
+  linux_bulk: &linux_bulk
+    machine: true
+    environment:
+      BIOCONDA_LABEL: gcc7
   skip_fork: &skip_fork
     run:
       name: Check for fork
@@ -163,7 +174,7 @@ jobs:

   # build, test and upload for bulk branch on linux
   bulk-linux:
-    <<: *linux
+    <<: *linux_bulk
     steps:
       - *fail_fork
       - checkout
@@ -175,11 +186,12 @@ jobs:
           name: Building, testing, and uploading of all unpublished recipes
           command: |
             bioconda-utils build recipes config.yml \
-              --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
+              --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
+              --check-channels conda-forge/label/gcc7 bioconda/label/gcc7 bioconda

   # build, test and upload for bulk branch on macos
   bulk-macos:
-    <<: *macos
+    <<: *macos_bulk
     steps:
       - *fail_fork
       - checkout
@@ -191,7 +203,8 @@ jobs:
           name: Building, testing and uploading of all unpublished recipes
           command: |
             bioconda-utils build recipes config.yml \
-              --anaconda-upload
+              --anaconda-upload \
+              --check-channels conda-forge/label/gcc7 bioconda/label/gcc7 bioconda

   # nightly build, test and upload of unpublished recipes on linux
   nightly-upload-linux:

The BIOCONDA_LABEL environment variable can now be used to set upload labels (not setting it should result in no change in behavior). Note that by adding channels to config.yml in bulk, we then need to explicitly set --check-channels, since otherwise bulk will try to build everything (it takes the first two channels from config.yml by default and I'd like the new gcc7 label to take priority in the off-chance that any packages are already in the main bioconda channel.

@bgruening This should of course only be merged once bioconda-common has been updated. Since this is a rather large change it'd be good to babysit the first build to ensure the packages are going to the appropriate label. I won't be appropriately available until after ~8 tonight, so unless you want to keep an eye on things please don't merge until then.

[bgruening]

Could we just take one recipe and the circle-ci changes and see how this behaves. If this one recipe build and gets the correct label, we can proceed with this PR?

[dpryan79]

That would indeed be easier :) I'll do that later if you don't first.

[bgruening]

This one needs a rebase and then I think we are ready to go :)

[dpryan79]

git merge -s ours bulk (after copying over the one change I made in bulk) is easier than figuring out how to rebase across branches where there have been multiple merges.

[bgruening]

Sleep well @dpryan79. I will watch the logs a little bit and then merge before I go to bed.

[bgruening]

Thanks!!!