new manifest, mosek, changes to build.xml

build.xml

@@ -6,7 +6,7 @@
 <target name="create-zip" depends="init">
     <antcall target="prezip"/>
     <zip destfile="${dest.dir}/${ant.project.name}.zip" whenempty="fail" defaultexcludes="true">
-        <fileset dir="." includes="manifest, paramgroups.json, LICENSE"/>
+        <fileset dir="." includes="manifest, paramgroups.json, LICENSE, mosek.lic"/>
         <!-- if you are iterating in the module integrator you will need to include the source files in the module zip -->
         <!-- zipfileset dir="src" includes="*.py"/-->
     </zip>

manifest

@@ -1,10 +1,10 @@
 #AmpliconSuite
-#Wed Jan 10 13:27:32 PST 2024
+#Tue Jan 30 14:01:53 PST 2024
 JVMLevel=
-LSID=urn\:lsid\:genepattern.org\:module.analysis\:00427\:33
+LSID=urn\:lsid\:genepattern.org\:module.analysis\:00427\:37.1
 author=Edwin Huang;Mesirov Lab
 categories=ecdna
-commandLine=python3 /opt/genepatt/run_aa.py --input <AA_zipped_output> <bam.file> <fastq.r1> <fastq.r2> --n_threads <job.cpuCount>  <no.filter>  <skip.QC>  <VCF.no.filter> --reference <reference> --file_prefix <Output.File.Prefix> --RUN_AA <RUN.AA> --RUN_AC <RUN.AC> --min_outputs  <minimal.outputs>  <ploidy>  <purity>  <cnvkit.segmentation>  <AA.seed>  <CN.gain>  <Minimum.copy.number.size>   <Downsample.Argument>  <AA.runmode>  <AA.extend.mode>  <AA.std.of.insert.size>  <cnv.bed>  <normal_bam>  <VCF.file>   <sample_metadata>  <sample_type>  <tissue_of_origin>  <sample_description>  <reference_genome>  <run_metadata_file>  <number_of_AA_amplicons>  <sample_source>  <number_of_AA_features> --path_to_mosek /expanse/projects/mesirovlab/genepattern/servers/ucsd.prod/mosek/8/licenses/
+commandLine=python3 /opt/genepatt/run_aa.py --input <AA_zipped_output> <bam.file> <fastq.r1> <fastq.r2> --n_threads <job.cpuCount>  <no.filter>  <skip.QC>  <VCF.no.filter> --reference <reference> --file_prefix <Output.File.Prefix> --RUN_AA <RUN.AA> --RUN_AC <RUN.AC> --min_outputs  <minimal.outputs>  <ploidy>  <purity>  <cnvkit.segmentation>  <AA.seed>  <CN.gain>  <Minimum.copy.number.size>   <Downsample.Argument>  <AA.runmode>  <AA.extend.mode>  <AA.std.of.insert.size>  <cnv.bed>  <normal_bam>  <VCF.file>   <sample_metadata>  <sample_type>  <tissue_of_origin>  <sample_description>  <reference_genome>  <run_metadata_file>  <number_of_AA_amplicons>  <sample_source>  <number_of_AA_features> --path_to_mosek <libdir>
 cpuType=any
 description=A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process.\n\nAll credits go to\: https\://github.com/jluebeck/PrepareAA \n\n\nView licenses here\: https\://github.com/genepattern/AmpliconSuite\#licenses\n<br/>\n<p>\nTo increase your GenePattern disk space quote so you can more easily upload the input bam files, <b><a href\="https\://forms.gle/23tkh98vwkhtCeKM7">click here to join the AmpliconSuiteUsers group on this server.</b> </a> </p>\n \n To run multiple samples at once, simply drag and drop multiple samples into the input options. There is no need to check the "Batch" box. 
 documentationUrl=https\://github.com/jluebeck/PrepareAA
@@ -244,7 +244,7 @@ p26_TYPE=TEXT
 p26_default_value=
 p26_description=
 p26_fileFormat=
-p26_flag=--metadata_sample_type 
+p26_flag=--metadata_sample_type
 p26_name=sample_type
 p26_numValues=0..1
 p26_optional=on
@@ -460,8 +460,8 @@ p9_prefix=--cnvkit_segmentation
 p9_prefix_when_specified=--cnvkit_segmentation 
 p9_type=java.lang.String
 p9_value=cbs\=cbs;haar\=haar;hmm\=hmm;hmm-tumor\=hmm-tumor;hmm-germline\=hmm-germline;none\=none
-privacy=private
-publicationDate=01/08/2024 11\:57 
+privacy=public
+publicationDate=01/17/2024 17\:02 
 quality=production
 src.repo=https\://github.com/genepattern/AmpliconSuite
 taskDoc=

mosek.lic

@@ -0,0 +1,21 @@
+#
+# MOSEK Personal Academic License (SN-c738a9aa-a321-4cb6-9533-1b241c2d694b)
+# https://www.mosek.com/products/license-agreement/
+# 2023 Mosek ApS - All rights reserved
+#
+
+VENDOR MOSEKLM
+FEATURE PTS MOSEKLM 10 13-dec-2024 uncounted VENDOR_STRING=-1*-1*-1*0 \
+	HOSTID=DEMO TS_OK SIGN="1413 08F8 A357 6CF6 9684 8ABA 0620 \
+	82F2 276E AB7E BA82 8A6E 4BCA 2DAE EE12 138A 355D F9B7 561A \
+	036D EC1E 2763 A9ED 9A78 6171 D017 3AA5 9E80 DEFC D7BE" \
+	SIGN2="0CB7 C03D 00D5 9C1C 5EBA 776E FB96 6208 6F32 12AE 001F \
+	FAA7 FD7F 2A0F 7B56 0449 DB65 9E20 4BE0 8D73 A24C 3220 5962 \
+	34E3 7724 EF9E 37C1 6ED4 67CD 2AA1"
+FEATURE PTON MOSEKLM 10 13-dec-2024 uncounted \
+	VENDOR_STRING=-1*-1*-1*0 HOSTID=DEMO TS_OK SIGN="14F0 E4A9 \
+	B640 B8BD 6194 AFFF 9848 F613 A685 486E EB11 DE82 2F30 7E2A \
+	38A5 1C35 93F4 A496 F46A CC12 F582 A56D 7E0B EAF9 4942 34BC \
+	194B B2BA E038 88DA" SIGN2="1E84 C15C A5AE 4E06 B508 D5CE 6771 \
+	B891 F5E6 B7BA 87FE E3FC BF49 08F3 7625 1C17 215F C33E AFBB \
+	462D 452B F6A2 96DB DFFC EB81 33D1 BEF2 0FC4 B5E5 54D4"