From 9f21998d9e0e907990d003eb547e29931251a7dc Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 22 May 2017 09:19:55 +0200 Subject: [PATCH 1/3] added automated install of dbnsfp/dbscsnv conf files, updated GRCh37 vcfanno git hash --- ggd-recipes/GRCh37/vcfanno.yaml | 4 ++++ ggd-recipes/hg38-noalt/vcfanno.yaml | 1 + ggd-recipes/hg38/vcfanno.yaml | 5 +++++ 3 files changed, 10 insertions(+) create mode 120000 ggd-recipes/hg38-noalt/vcfanno.yaml diff --git a/ggd-recipes/GRCh37/vcfanno.yaml b/ggd-recipes/GRCh37/vcfanno.yaml index e888804c..63c2307b 100644 --- a/ggd-recipes/GRCh37/vcfanno.yaml +++ b/ggd-recipes/GRCh37/vcfanno.yaml @@ -19,9 +19,13 @@ recipe: bcbio_baseurl=https://github.com/chapmanb/bcbio-nextgen/raw/$bcbio_githash/config/vcfanno wget --no-check-certificate -O rnaedit.conf -c $bcbio_baseurl/GRCh37-rnaedit.conf wget --no-check-certificate -O rnaedit.lua -c $bcbio_baseurl/GRCh37-rnaedit.lua + wget --no-check-certificate -O dbnsfp.conf -c $bcbio_baseurl/GRCh37-dbnsfp.conf + wget --no-check-certificate -O dbscsnv.conf -c $bcbio_baseurl/GRCh37-dbscsnv.conf recipe_outfiles: - config/vcfanno/gemini.lua - config/vcfanno/gemini.conf - config/vcfanno/rnaedit.lua - config/vcfanno/rnaedit.conf + - config/vcfanno/dbnsfp.conf + - config/vcfanno/dbscsnv.conf diff --git a/ggd-recipes/hg38-noalt/vcfanno.yaml b/ggd-recipes/hg38-noalt/vcfanno.yaml new file mode 120000 index 00000000..69c81b4e --- /dev/null +++ b/ggd-recipes/hg38-noalt/vcfanno.yaml @@ -0,0 +1 @@ +../hg38/vcfanno.yaml \ No newline at end of file diff --git a/ggd-recipes/hg38/vcfanno.yaml b/ggd-recipes/hg38/vcfanno.yaml index c59d3c08..17aadb3f 100644 --- a/ggd-recipes/hg38/vcfanno.yaml +++ b/ggd-recipes/hg38/vcfanno.yaml @@ -15,7 +15,12 @@ recipe: bcbio_baseurl=https://github.com/chapmanb/bcbio-nextgen/raw/$githash/config/vcfanno/ wget --no-check-certificate -O gemini.conf -c $bcbio_baseurl/hg38-gemini.conf wget --no-check-certificate -O gemini.lua -c $bcbio_baseurl/hg38-gemini.lua + wget --no-check-certificate -O dbnsfp.conf -c $bcbio_baseurl/hg38-dbnsfp.conf + wget --no-check-certificate -O dbscsnv.conf -c $bcbio_baseurl/hg38-dbscsnv.conf + recipe_outfiles: - config/vcfanno/gemini.lua - config/vcfanno/gemini.conf + - config/vcfanno/dbnsfp.conf + - config/vcfanno/dbscsnv.conf From 8000ccf878cba91d18d1dadb9f480a9c3ca9224a Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 22 May 2017 11:40:50 +0200 Subject: [PATCH 2/3] updated bcbio git hash for vcfanno configs --- ggd-recipes/GRCh37/vcfanno.yaml | 2 +- ggd-recipes/hg38/vcfanno.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ggd-recipes/GRCh37/vcfanno.yaml b/ggd-recipes/GRCh37/vcfanno.yaml index 63c2307b..95e8f9c7 100644 --- a/ggd-recipes/GRCh37/vcfanno.yaml +++ b/ggd-recipes/GRCh37/vcfanno.yaml @@ -10,7 +10,7 @@ recipe: recipe_cmds: - | vcfanno_githash=5fcce8db2aeee016ab927c8ca36a715c02f982f9 - bcbio_githash=13ef069207dbd6fa5f85c09c4ad8de176b74c39e + bcbio_githash=5bcfde79c083d5c34f13f81fe578b4606a7cc80c mkdir -p config/vcfanno cd config/vcfanno gemini_baseurl=https://github.com/brentp/vcfanno/raw/$vcfanno_githash/example diff --git a/ggd-recipes/hg38/vcfanno.yaml b/ggd-recipes/hg38/vcfanno.yaml index 17aadb3f..7fcfc92e 100644 --- a/ggd-recipes/hg38/vcfanno.yaml +++ b/ggd-recipes/hg38/vcfanno.yaml @@ -9,7 +9,7 @@ recipe: recipe_type: bash recipe_cmds: - | - githash=ac5890aab096370d41c276d747e6f9eef0bf0867 + githash=5bcfde79c083d5c34f13f81fe578b4606a7cc80c mkdir -p config/vcfanno cd config/vcfanno bcbio_baseurl=https://github.com/chapmanb/bcbio-nextgen/raw/$githash/config/vcfanno/ From 835479be00168c1bf7929340529ffe152a74e9ee Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Mon, 22 May 2017 11:51:37 +0200 Subject: [PATCH 3/3] updated vcfanno config version numbers --- ggd-recipes/GRCh37/vcfanno.yaml | 2 +- ggd-recipes/hg38/vcfanno.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ggd-recipes/GRCh37/vcfanno.yaml b/ggd-recipes/GRCh37/vcfanno.yaml index 95e8f9c7..fed1d8e5 100644 --- a/ggd-recipes/GRCh37/vcfanno.yaml +++ b/ggd-recipes/GRCh37/vcfanno.yaml @@ -3,7 +3,7 @@ --- attributes: name: vcfanno - version: 20170331 + version: 20170522 recipe: full: recipe_type: bash diff --git a/ggd-recipes/hg38/vcfanno.yaml b/ggd-recipes/hg38/vcfanno.yaml index 7fcfc92e..d55a58b4 100644 --- a/ggd-recipes/hg38/vcfanno.yaml +++ b/ggd-recipes/hg38/vcfanno.yaml @@ -3,7 +3,7 @@ --- attributes: name: vcfanno - version: 20170110 + version: 20170522 recipe: full: recipe_type: bash