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Update release 100 branch with all the latest commits from master

Merged Update release 100 branch with all the latest commits from master
master into release/100
Merged Marek Szuba requested to merge master into release/100
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roles/rest/tasks/comparahal.yml
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@@ -11,13 +11,13 @@
when: HAL_Makefile.stdout.find('PROGRESSIVE_CACTUS_DIR') != -1
- name: Make the Compara progressiveCactus HAL XS bindings, new way
shell: ". {{ PERL_RC | default('~/.bashrc') }} && {{ compara_halxs_makefile }} {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/hdf5 {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/sonLib {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/hal && make"
shell: ". {{ PERL_RC | default('~/.bashrc') }} && perl {{ compara_halxs_makefile }} {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/hdf5 {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/sonLib {{ PROGRESSIVE_CACTUS_DIR | default(PROGRESSIVE_CACTUS_DEFAULT) }}/submodules/hal && make"
args:
chdir: "{{ ensembl_install_dir }}/ensembl-compara/modules/Bio/EnsEMBL/Compara/HAL/HALXS"
when: HAL_Makefile.stdout.find('Need to run this makefile with 3 paths') != -1
- name: Make the Compara progressiveCactus HAL XS bindings, the linuxbrew way
shell: ". {{ PERL_RC | default('~/.bashrc') }} && {{ compara_halxs_makefile }} {{ linuxbrew_home }} && make"
shell: ". {{ PERL_RC | default('~/.bashrc') }} && perl {{ compara_halxs_makefile }} {{ linuxbrew_home }} && make"
args:
chdir: "{{ ensembl_install_dir }}/ensembl-compara/modules/Bio/EnsEMBL/Compara/HAL/HALXS"
when: HAL_Makefile.stdout.find('The path to the linuxbrew installation must be provided') != -1