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tverbeirentverbeiren
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Minor update to 0-... after test
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‎VCF_Comp/0-Setup.snb

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@@ -41,7 +41,7 @@
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 4
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"execution_count" : 1
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} ]
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}, {
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"metadata" : {
@@ -82,14 +82,14 @@
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "total 91951\ndrwxr-xr-x 6 root root 204 May 31 12:19 .\ndrwxrwxr-x 10 daemon daemon 4096 Jun 7 12:06 ..\n-rw------- 1 root root 1860660 May 31 12:04 8122_N.vcf.gz\n-rw------- 1 root root 1888646 May 31 12:05 8122_T.vcf.gz\n-rw------- 1 root root 45003812 May 31 12:02 snpEff.8122_N.vcf.gz\n-rw------- 1 root root 45398741 May 31 12:02 snpEff.8122_T.vcf.gz\n\nimport sys.process._\n"
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"text" : "total 91951\ndrwxr-xr-x 6 root root 204 May 31 12:19 .\ndrwxrwxr-x 11 daemon daemon 4096 Jun 7 19:53 ..\n-rw------- 1 root root 1860660 May 31 12:04 8122_N.vcf.gz\n-rw------- 1 root root 1888646 May 31 12:05 8122_T.vcf.gz\n-rw------- 1 root root 45003812 May 31 12:02 snpEff.8122_N.vcf.gz\n-rw------- 1 root root 45398741 May 31 12:02 snpEff.8122_T.vcf.gz\n\nimport sys.process._\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/plain" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 4
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"execution_count" : 3
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} ]
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}, {
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"metadata" : {
@@ -103,14 +103,14 @@
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "total 5\ndrwxr-xr-x 3 root root 102 Jun 7 12:19 .\ndrwxrwxr-x 10 daemon daemon 4096 Jun 7 12:20 ..\n-rw-r--r-- 1 root root 122 Jun 7 11:45 README.md\n\nimport sys.process._\n"
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"text" : "total 5\ndrwxr-xr-x 2 root root 68 Jun 7 19:15 .\ndrwxrwxr-x 11 daemon daemon 4096 Jun 7 19:53 ..\n\nimport sys.process._\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/plain" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 3
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"execution_count" : 4
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} ]
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}, {
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"metadata" : {
@@ -137,7 +137,7 @@
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 2
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"execution_count" : 5
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} ]
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}, {
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"metadata" : {
@@ -151,7 +151,7 @@
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"input_collapsed" : false,
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"collapsed" : false,
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"presentation" : {
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"tabs_state" : "{\n \"tab_id\": \"#tab368404145-0\"\n}",
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"tabs_state" : "{\n \"tab_id\": \"#tab471348600-0\"\n}",
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"pivot_chart_state" : "{\n \"hiddenAttributes\": [],\n \"menuLimit\": 200,\n \"cols\": [],\n \"rows\": [],\n \"vals\": [],\n \"exclusions\": {},\n \"inclusions\": {},\n \"unusedAttrsVertical\": 85,\n \"autoSortUnusedAttrs\": false,\n \"inclusionsInfo\": {},\n \"aggregatorName\": \"Count\",\n \"rendererName\": \"Table\"\n}"
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},
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"id" : "4CC4B4E7E5624439A1840154B718D119"
@@ -161,14 +161,14 @@
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "res5: Array[Array[String]] = Array(Array(#CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, 0), Array(1, 69428, ., T, G, 505.32, ., AC=1;AF=0.50;AN=2;BaseQRankSum=-3.890;DP=157;DS;Dels=0.00;FS=15.860;HRun=0;HaplotypeScore=5.4661;MQ=20.94;MQ0=52;MQRankSum=-0.024;QD=3.22;ReadPosRankSum=1.722;SB=-34.00, GT:AD:DP:GQ:PL, 0/1:118,39:157:99:535,0,1354), Array(1, 69511, ., A, G, 3066.29, ., AC=2;AF=1.00;AN=2;BaseQRankSum=-0.884;DP=165;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9979;MQ=28.65;MQ0=21;MQRankSum=-1.078;QD=18.58;ReadPosRankSum=-0.206;SB=-923.15, GT:AD:DP:GQ:PL, 1/1:1,163:164:99:3099,310,0), Array(1, 325075, ., G, C, 41.01, ., AC=1;AF=0.50;AN=2;BaseQRankSum=-0.727;DP=84;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=6.33;MQ0=80;MQRankSum=-0.727;QD=0.49;ReadPosRankSum=0.727;..."
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"text" : "res9: Array[Array[String]] = Array(Array(#CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, 0), Array(1, 69428, ., T, G, 505.32, ., AC=1;AF=0.50;AN=2;BaseQRankSum=-3.890;DP=157;DS;Dels=0.00;FS=15.860;HRun=0;HaplotypeScore=5.4661;MQ=20.94;MQ0=52;MQRankSum=-0.024;QD=3.22;ReadPosRankSum=1.722;SB=-34.00, GT:AD:DP:GQ:PL, 0/1:118,39:157:99:535,0,1354), Array(1, 69511, ., A, G, 3066.29, ., AC=2;AF=1.00;AN=2;BaseQRankSum=-0.884;DP=165;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9979;MQ=28.65;MQ0=21;MQRankSum=-1.078;QD=18.58;ReadPosRankSum=-0.206;SB=-923.15, GT:AD:DP:GQ:PL, 1/1:1,163:164:99:3099,310,0), Array(1, 325075, ., G, C, 41.01, ., AC=1;AF=0.50;AN=2;BaseQRankSum=-0.727;DP=84;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=6.33;MQ0=80;MQRankSum=-0.727;QD=0.49;ReadPosRankSum=0.727;..."
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : "<div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anon49f699378275986f019db1d9a67bd7b8&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;368404145&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/tabs'], \n function(playground, _magictabs) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magictabs,\n \"o\": {}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <div>\n <ul class=\"nav nav-tabs\" id=\"ul368404145\"><li>\n <a href=\"#tab368404145-0\"><i class=\"fa fa-table\"/></a>\n </li><li>\n <a href=\"#tab368404145-1\"><i class=\"fa fa-cubes\"/></a>\n </li></ul>\n\n <div class=\"tab-content\" id=\"tab368404145\"><div class=\"tab-pane\" id=\"tab368404145-0\">\n <div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anon22d5e87e9dcf971fbc19f2e1daa29527&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;541530102&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/tableChart'], \n function(playground, _magictableChart) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magictableChart,\n \"o\": {\"headers\":[],\"width\":600,\"height\":400}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon443b11d1a7cbe2282fb7e06a182507ee&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p> <span style=\"color:red\"><p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon5568c1e9eda91e2c6d1f7ee91916ae74&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p></span>\n <div>\n </div>\n </div></div>\n </div><div class=\"tab-pane\" id=\"tab368404145-1\">\n <div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anon6eb952bb6f24518ea5562ad4b270755c&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;2126025887&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/pivotChart'], \n function(playground, _magicpivotChart) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magicpivotChart,\n \"o\": {\"width\":600,\"height\":400,\"derivedAttributes\":{},\"extraOptions\":{}}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon9fcafa16831aeab41ec5bb50ca7453e7&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p> <span style=\"color:red\"><p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon5196c1ad90fdefab3a9c09e2f0a79ba5&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p></span>\n <div>\n </div>\n </div></div>\n </div></div>\n </div>\n </div></div>"
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"text/html" : "<div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anonbcdea51f907935a2739f45d930719b9b&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;471348600&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/tabs'], \n function(playground, _magictabs) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magictabs,\n \"o\": {}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <div>\n <ul class=\"nav nav-tabs\" id=\"ul471348600\"><li>\n <a href=\"#tab471348600-0\"><i class=\"fa fa-table\"/></a>\n </li><li>\n <a href=\"#tab471348600-1\"><i class=\"fa fa-cubes\"/></a>\n </li></ul>\n\n <div class=\"tab-content\" id=\"tab471348600\"><div class=\"tab-pane\" id=\"tab471348600-0\">\n <div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anon81df6e3d2cbb967b64052c5c924d90a0&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;357507200&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/tableChart'], \n function(playground, _magictableChart) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magictableChart,\n \"o\": {\"headers\":[],\"width\":600,\"height\":400}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon22f6f3cbdcb4a1a0b4cdd915223bcd5a&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p> <span style=\"color:red\"><p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon1f7ab141fed4b51932f16485f2210eb8&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p></span>\n <div>\n </div>\n </div></div>\n </div><div class=\"tab-pane\" id=\"tab471348600-1\">\n <div>\n <script data-this=\"{&quot;dataId&quot;:&quot;anon664a1cdf54044dc05eba1e0cfd922e82&quot;,&quot;dataInit&quot;:[{},{},{},{},{}],&quot;genId&quot;:&quot;1760325361&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/req(['../javascripts/notebook/playground','../javascripts/notebook/magic/pivotChart'], \n function(playground, _magicpivotChart) {\n // data ==> data-this (in observable.js's scopedEval) ==> this in JS => { dataId, dataInit, ... }\n // this ==> scope (in observable.js's scopedEval) ==> this.parentElement ==> div.container below (toHtml)\n\n playground.call(data,\n this\n ,\n {\n \"f\": _magicpivotChart,\n \"o\": {\"width\":600,\"height\":400,\"derivedAttributes\":{},\"extraOptions\":{}}\n }\n \n \n \n );\n }\n );/*]]>*/</script>\n <div>\n <p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anonaed579d1d9b936b8cc20efba316e45c5&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p> <span style=\"color:red\"><p data-bind=\"text: value\"><script data-this=\"{&quot;valueId&quot;:&quot;anon5b6fa94ce480023249f3098a2c64abb4&quot;}\" type=\"text/x-scoped-javascript\">/*<![CDATA[*/\nreq(\n['observable', 'knockout'],\nfunction (O, ko) {\n ko.applyBindings({\n value: O.makeObservable(valueId)\n },\n this\n );\n});\n /*]]>*/</script></p></span>\n <div>\n </div>\n </div></div>\n </div></div>\n </div>\n </div></div>"
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},
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"output_type" : "execute_result",
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"execution_count" : 3
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"execution_count" : 6
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} ]
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}, {
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"metadata" : {
@@ -213,14 +213,14 @@
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "Running in Docker, checking wget and unzip dependencies...\nInstalling wget\nInstalling unzip\nres7: AnyVal = 0\n"
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"text" : "Running in Docker, checking wget and unzip dependencies...\nInstalling wget\nInstalling unzip\nres11: AnyVal = 0\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : "0"
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},
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"output_type" : "execute_result",
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"execution_count" : 5
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"execution_count" : 7
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} ]
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}, {
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"metadata" : {
@@ -230,29 +230,19 @@
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"id" : "EC30FE5830904E588DEAA28BE132DACA"
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},
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"cell_type" : "code",
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"source" : "val snpEffDownloaded = \n if (!snpEffInstalled) {\n println(\"Downloading from Sourceforge...\")\n shellTestToBool(s\"wget http://heanet.dl.sourceforge.net/project/snpeff/${snpEffSourceZip} -P ${snpEffBaseDir}\")\n } else true\n\n// If the download is not successfull, remove the stale file\nif (!snpEffDownloaded) shellTestToBool(s\"rm ${snpEffBaseDir}${snpEffSourceZip}\")\n\nif (!snpEffInstalled && snpEffDownloaded) {\n println(\"Unzipping snpEff...\") \n shellTestToBool(s\"unzip ${snpEffBaseDir}${snpEffSourceZip} -d ${projectDir}\")\n}\n\n\n\n\n",
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"source" : "val snpEffDownloaded = \n if (!snpEffInstalled) {\n println(\"Downloading from Sourceforge...\")\n shellTestToBool(s\"wget http://heanet.dl.sourceforge.net/project/snpeff/${snpEffSourceZip} -P ${snpEffBaseDir}\")\n } else true\n\n// If the download is not successfull, remove the stale file\nif (!snpEffDownloaded) shellTestToBool(s\"rm ${snpEffBaseDir}${snpEffSourceZip}\")\n\nif (!snpEffInstalled && snpEffDownloaded) {\n println(\"Unzipping snpEff...\") \n shellTestToBool(s\"unzip ${snpEffBaseDir}${snpEffSourceZip} -d ${projectDir}\")\n}",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "Downloading from Sourceforge...\nUnzipping snpEff...\nsnpEffDownloaded: Boolean = true\nres55: AnyVal = true\n"
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"text" : "Downloading from Sourceforge...\nUnzipping snpEff...\nsnpEffDownloaded: Boolean = true\nres13: AnyVal = true\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : "true"
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},
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"output_type" : "execute_result",
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"execution_count" : 34
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"execution_count" : 8
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} ]
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : true,
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"id" : "32FC02C2E3F147128283B90CB9245E50"
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},
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"cell_type" : "code",
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"source" : "",
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"outputs" : [ ]
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} ],
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"nbformat" : 4
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}

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