[ { "id": "tlex3", "name": "T-lex3", "article": "10.1093\/bioinformatics\/btz727", "website": "https:\/\/github.com\/GonzalezLab\/T-lex3", "git": "https:\/\/github.com\/GonzalezLab\/T-lex3", "description": "T-lex is a computational pipeline that detects presence and\/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data.", "version": "3.0", "documentation": "https:\/\/github.com\/GonzalezLab\/T-lex3\/blob\/master\/Manual.md", "multiqc": "custom", "commands": [ { "name": "tlex3", "cname": "Tlex3", "command": "tlex", "category": "blast", "output_dir": "tlex3", "inputs": [ { "name": "TE_list", "type": "path" }, { "name": "TE_annotations", "type": "path" }, { "name": "genome_fasta", "type": "contigs" }, { "name": "read_dir", "type": "dir" } ], "outputs": [ { "name": "Tresults", "type": "tlex", "file": "Tresults", "description": "T-lex3 results" } ], "options": [ { "name": "tlex3_te_list", "type": "input_file", "value": "", "multiple": false, "label": "Path to TE_list" }, { "name": "tlex3_te_annotations", "type": "input_file", "value": "", "multiple": false, "label": "Path to TE_annotations" }, { "name": "tlex3_genome_fasta", "type": "input_file", "accept": [ ".fasta", ".fa", ".fasta.gz", ".fa.gz" ], "value": "", "multiple": false, "label": "Path to reference genome fasta file" }, { "name": "tlex3_species", "prefix": "-s", "type": "text", "value": "", "label": "name the species studied ( default: drosophila, cf. RepeatMasker program)" } ] } ], "install": { "tlex3": [ "cd \/opt\/biotools", "git clone https:\/\/github.com\/GonzalezLab\/T-lex3.git", "mv T-lex3\/tlex-open-v3.0.pl bin\/tlex", "chmod +x bin\/tlex" ], "perl": [ "apt-get update", "apt-get install -y perl unzip bzip2 libkrb5-3", "wget http:\/\/security.ubuntu.com\/ubuntu\/pool\/main\/libp\/libpng\/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb && dpkg -i libpng12-0_1.2.54-1ubuntu1.1_amd64.deb", "apt-get clean -y" ], "rmblast&blast+": [ "cd \/opt\/biotools", "wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/rmblast\/2.2.28\/ncbi-rmblastn-2.2.28-x64-linux.tar.gz", "wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.9.0\/ncbi-blast-2.9.0+-x64-linux.tar.gz", "tar -xzf ncbi-rmblastn*", "tar -xzf ncbi-blast*", "mv ncbi*\/bin\/* bin", "rm -rf ncbi*" ], "trf": [ "cd \/opt\/biotools ", "wget http:\/\/tandem.bu.edu\/trf\/downloads\/trf407b.linux64", "mv trf*.linux64 bin\/trf", "chmod +x bin\/trf" ], "repeatmasker": [ "cd \/opt\/biotools", "wget http:\/\/www.repeatmasker.org\/RepeatMasker-open-4-0-9-p2.tar.gz", "tar -xzf RepeatMasker-open-4-0-9-p2.tar.gz", "rm -rf RepeatMasker-open-4-0-9-p2.tar.gz", "perl -0p -e 's\/\\\/usr\\\/local\\\/hmmer\/\\\/usr\\\/bin\/g;' -e 's\/\\\/usr\\\/local\\\/rmblast\/\\\/opt\\\/biotools\\\/bin\/g;' -e 's\/DEFAULT_SEARCH_ENGINE = \"crossmatch\"\/DEFAULT_SEARCH_ENGINE = \"ncbi\"\/g;' -e 's\/TRF_PRGM = \"\"\/TRF_PRGM = \"\\\/opt\\\/biotools\\\/bin\\\/trf\"\/g;' RepeatMasker\/RepeatMaskerConfig.tmpl > RepeatMasker\/RepeatMaskerConfig.pm", "cd RepeatMasker", "perl -i -0pe 's\/^#\\!.*perl.*\/#\\!\\\/usr\\\/bin\\\/env perl\/g' RepeatMasker DateRepeats ProcessRepeats RepeatProteinMask DupMasker util\/queryRepeatDatabase.pl util\/queryTaxonomyDatabase.pl util\/rmOutToGFF3.pl util\/rmToUCSCTables.pl", "cpan Text::Soundex", "ENV PATH $PATH:\/opt\/biotools\/RepeatMasker" ], "shrimp2": [ "cd \/opt\/biotools", "wget http:\/\/compbio.cs.toronto.edu\/shrimp\/releases\/SHRiMP_2_2_3.lx26.x86_64.tar.gz", "tar -xzf SHRiMP_2_2_3.lx26.x86_64.tar.gz", "rm -rf SHRiMP_2_2_3.lx26.x86_64.tar.gz", "ENV PATH $PATH:\/opt\/biotools\/SHRiMP_2_2_3" ], "blat": [ "cd \/opt\/biotools", "mkdir blat36", "wget https:\/\/hgwdev.gi.ucsc.edu\/~kent\/exe\/linux\/blatSuite.36.zip", "unzip blatSuite.36.zip -d \/opt\/biotools\/blat36", "rm -rf blatSuite.36.zip", "ENV PATH $PATH:\/opt\/biotools\/blat36" ], "samtools": [ "cd \/opt\/biotools", "wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2", "tar -xvjf samtools-1.9.tar.bz2", "cd samtools-1.9", ".\/configure && make", "cd ..", "mv samtools-1.9\/samtools bin\/samtools", "rm -r samtools-1.9 samtools-1.9.tar.bz2" ], "bcftools": [ "cd \/opt\/biotools", "wget https:\/\/github.com\/samtools\/bcftools\/releases\/download\/1.9\/bcftools-1.9.tar.bz2", "tar -xvjf bcftools-1.9.tar.bz2", "cd bcftools-1.9", ".\/configure --prefix=\/opt\/biotools", "make -j 10", "make install", "mv bcftools \/opt\/biotools\/bin\/", "cd .. && rm -r bcftools-1.9.tar.bz2 bcftools-1.9" ], "bwa": [ "cd \/opt\/biotools", "wget https:\/\/github.com\/lh3\/bwa\/releases\/download\/v0.7.17\/bwa-0.7.17.tar.bz2", "tar -xvjf bwa-0.7.17.tar.bz2", "cd bwa-0.7.17", "make -j 10", "mv bwa ..\/bin\/", "cd ..", "rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2" ], "fastx_toolkit": [ "apt-get update -q", "apt-get install -y -qqq build-essential pkg-config autoconf", "cd \/tmp", "wget https:\/\/github.com\/agordon\/libgtextutils\/releases\/download\/0.7\/libgtextutils-0.7.tar.gz", "tar -xzf libgtextutils-0.7.tar.gz", "cd libgtextutils-0.7", ".\/reconf", ".\/configure", "make CXXFLAGS='-std=c++03'", "make install", "cd \/tmp", "wget https:\/\/github.com\/agordon\/fastx_toolkit\/releases\/download\/0.0.14\/fastx_toolkit-0.0.14.tar.bz2", "tar -xjf fastx_toolkit-0.0.14.tar.bz2", "cd fastx_toolkit-0.0.14", ".\/reconf", ".\/configure", "make", "make install", "apt-get remove -y -qqq build-essential pkg-config autoconf", "apt-get autoremove -y -qqq", "apt-get clean -y -qqq", "cd \/tmp", "rm -rf \/var\/lib\/apt\/lists\/*", "rm -rf \/tmp\/*" ], "emboss": [ "apt-get update -q", "apt-get install -y emboss", "apt-get clean -y" ], "fastagrep": [ "cd \/tmp", "wget http:\/\/bioinfo.ut.ee\/download\/dl.php?file=28 -O fastagrep.tar.gz", "tar -xzf fastagrep.tar.gz", "mv .\/fastagrep_v2.0_64bit_linux_2_6 \/opt\/biotools\/bin\/fastagrep", "rm -rf fastagrep.tar.gz" ] }, "citations": { "tlex3": [ "Mar\u00eda Bogaerts-M\u00e1rquez, Maite G Barr\u00f3n, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Ra\u00fal Castanera, Josep M Casacuberta, Josefa Gonz\u00e1lez, T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data, Bioinformatics, Volume 36, Issue 4, 15 February 2020, Pages 1191-1197, https:\/\/doi.org\/10.1093\/bioinformatics\/btz727" ], "RepeatMasker": [ "RepeatMasker. version Open 3.2.8 A.F.A. Smit, R. Hubley & P. Green RepeatMasker" ], "SHRIMP2": [ "David M, Dzamba M, Lister D, Ilie L, Brudno M. (2011) SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics. Apr 1;27(7):1011-2. Epub 2011 Jan 28." ], "BLAT": [ "Kent W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res. 12:656-664" ], "samtools": [ "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352" ], "bcftools": [ "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509" ], "bwa": [ "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324" ], "bwa-mem": [ "Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]" ] }, "yaml": "{\n id: tlex3,\n name: T-lex3,\n article: 10.1093\/bioinformatics\/btz727,\n website: \"https:\/\/github.com\/GonzalezLab\/T-lex3\",\n git: \"https:\/\/github.com\/GonzalezLab\/T-lex3\",\n description: \"T-lex is a computational pipeline that detects presence and\/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data.\",\n version: \"3.0\",\n documentation: \"https:\/\/github.com\/GonzalezLab\/T-lex3\/blob\/master\/Manual.md\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: tlex3,\n cname: \"Tlex3\",\n command: tlex,\n category: \"blast\",\n output_dir: tlex3,\n inputs: [{ name: TE_list, type: \"path\" }, { name: TE_annotations, type: \"path\" }, { name: genome_fasta, type: \"contigs\" }, { name: read_dir, type: \"dir\" }],\n outputs: [\n { name: Tresults, type: \"tlex\", file: Tresults, description: \"T-lex3 results\" }\n ],\n options:\n [\n {\n name: tlex3_te_list,\n type: input_file,\n value: \"\",\n multiple: FALSE,\n label: \"Path to TE_list\",\n },\n {\n name: tlex3_te_annotations,\n type: input_file,\n value: \"\",\n multiple: FALSE,\n label: \"Path to TE_annotations\",\n },\n {\n name: tlex3_genome_fasta,\n type: input_file,\n accept: [\".fasta\",\".fa\",\".fasta.gz\",\".fa.gz\"],\n value: \"\",\n multiple: FALSE,\n label: \"Path to reference genome fasta file\",\n },\n {\n name: tlex3_species,\n prefix: -s,\n type: text,\n value: \"\",\n label: \"name the species studied ( default: drosophila, cf. RepeatMasker program)\",\n },\n ]\n },\n ],\n install: {\n tlex3: [\n \"cd \/opt\/biotools\",\n \"git clone https:\/\/github.com\/GonzalezLab\/T-lex3.git\",\n \"mv T-lex3\/tlex-open-v3.0.pl bin\/tlex\",\n \"chmod +x bin\/tlex\"\n ],\n # perl and libs\n perl: [\n \"apt-get update\",\n \"apt-get install -y perl unzip bzip2 libkrb5-3\",\n \"wget http:\/\/security.ubuntu.com\/ubuntu\/pool\/main\/libp\/libpng\/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb && dpkg -i libpng12-0_1.2.54-1ubuntu1.1_amd64.deb\",\n \"apt-get clean -y\"\n ],\n rmblast&blast+: [\n \"cd \/opt\/biotools\",\n \"wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/rmblast\/2.2.28\/ncbi-rmblastn-2.2.28-x64-linux.tar.gz\",\n \"wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.9.0\/ncbi-blast-2.9.0+-x64-linux.tar.gz\",\n \"tar -xzf ncbi-rmblastn*\",\n \"tar -xzf ncbi-blast*\",\n \"mv ncbi*\/bin\/* bin\",\n \"rm -rf ncbi*\",\n ],\n trf: [\n \"cd \/opt\/biotools \",\n \"wget http:\/\/tandem.bu.edu\/trf\/downloads\/trf407b.linux64\",\n \"mv trf*.linux64 bin\/trf\",\n \"chmod +x bin\/trf\"\n ],\n repeatmasker: [\n \"cd \/opt\/biotools\",\n \"wget http:\/\/www.repeatmasker.org\/RepeatMasker-open-4-0-9-p2.tar.gz\",\n \"tar -xzf RepeatMasker-open-4-0-9-p2.tar.gz\",\n \"rm -rf RepeatMasker-open-4-0-9-p2.tar.gz\",\n \"perl -0p -e 's\/\\\\\/usr\\\\\/local\\\\\/hmmer\/\\\\\/usr\\\\\/bin\/g;' -e 's\/\\\\\/usr\\\\\/local\\\\\/rmblast\/\\\\\/opt\\\\\/biotools\\\\\/bin\/g;' -e 's\/DEFAULT_SEARCH_ENGINE = \\\"crossmatch\\\"\/DEFAULT_SEARCH_ENGINE = \\\"ncbi\\\"\/g;' -e 's\/TRF_PRGM = \\\"\\\"\/TRF_PRGM = \\\"\\\\\/opt\\\\\/biotools\\\\\/bin\\\\\/trf\\\"\/g;' RepeatMasker\/RepeatMaskerConfig.tmpl > RepeatMasker\/RepeatMaskerConfig.pm\",\n \"cd RepeatMasker\",\n \"perl -i -0pe 's\/^#\\\\!.*perl.*\/#\\\\!\\\\\/usr\\\\\/bin\\\\\/env perl\/g' RepeatMasker DateRepeats ProcessRepeats RepeatProteinMask DupMasker util\/queryRepeatDatabase.pl util\/queryTaxonomyDatabase.pl util\/rmOutToGFF3.pl util\/rmToUCSCTables.pl\",\n \"cpan Text::Soundex\",\n \"ENV PATH $PATH:\/opt\/biotools\/RepeatMasker\"\n ],\n shrimp2: [\n \"cd \/opt\/biotools\",\n \"wget http:\/\/compbio.cs.toronto.edu\/shrimp\/releases\/SHRiMP_2_2_3.lx26.x86_64.tar.gz\",\n \"tar -xzf SHRiMP_2_2_3.lx26.x86_64.tar.gz\",\n \"rm -rf SHRiMP_2_2_3.lx26.x86_64.tar.gz\",\n \"ENV PATH $PATH:\/opt\/biotools\/SHRiMP_2_2_3\"\n ],\n blat: [\n \"cd \/opt\/biotools\",\n \"mkdir blat36\",\n \"wget https:\/\/hgwdev.gi.ucsc.edu\/~kent\/exe\/linux\/blatSuite.36.zip\",\n \"unzip blatSuite.36.zip -d \/opt\/biotools\/blat36\",\n \"rm -rf blatSuite.36.zip\",\n \"ENV PATH $PATH:\/opt\/biotools\/blat36\"\n ],\n samtools: [\n \"cd \/opt\/biotools\",\n \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n \"tar -xvjf samtools-1.9.tar.bz2\",\n \"cd samtools-1.9\",\n \".\/configure && make\",\n \"cd ..\",\n \"mv samtools-1.9\/samtools bin\/samtools\",\n \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n ],\n bcftools: [\n \"cd \/opt\/biotools\",\n \"wget https:\/\/github.com\/samtools\/bcftools\/releases\/download\/1.9\/bcftools-1.9.tar.bz2\",\n \"tar -xvjf bcftools-1.9.tar.bz2\",\n \"cd bcftools-1.9\",\n \".\/configure --prefix=\/opt\/biotools\",\n \"make -j 10\",\n \"make install\",\n \"mv bcftools \/opt\/biotools\/bin\/\",\n \"cd .. && rm -r bcftools-1.9.tar.bz2 bcftools-1.9\"\n ],\n bwa: [\n \"cd \/opt\/biotools\",\n \"wget https:\/\/github.com\/lh3\/bwa\/releases\/download\/v0.7.17\/bwa-0.7.17.tar.bz2\",\n \"tar -xvjf bwa-0.7.17.tar.bz2\",\n \"cd bwa-0.7.17\",\n \"make -j 10\",\n \"mv bwa ..\/bin\/\",\n \"cd ..\",\n \"rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2\"\n ],\n fastx_toolkit: [\n \"apt-get update -q\",\n \"apt-get install -y -qqq build-essential pkg-config autoconf\",\n \"cd \/tmp\",\n \"wget https:\/\/github.com\/agordon\/libgtextutils\/releases\/download\/0.7\/libgtextutils-0.7.tar.gz\",\n \"tar -xzf libgtextutils-0.7.tar.gz\",\n \"cd libgtextutils-0.7\",\n \".\/reconf\",\n \".\/configure\",\n \"make CXXFLAGS='-std=c++03'\",\n \"make install\",\n \"cd \/tmp\",\n \"wget https:\/\/github.com\/agordon\/fastx_toolkit\/releases\/download\/0.0.14\/fastx_toolkit-0.0.14.tar.bz2\",\n \"tar -xjf fastx_toolkit-0.0.14.tar.bz2\",\n \"cd fastx_toolkit-0.0.14\",\n \".\/reconf\",\n \".\/configure\",\n \"make\",\n \"make install\",\n \"apt-get remove -y -qqq build-essential pkg-config autoconf\",\n \"apt-get autoremove -y -qqq\",\n \"apt-get clean -y -qqq\",\n \"cd \/tmp\",\n \"rm -rf \/var\/lib\/apt\/lists\/*\",\n \"rm -rf \/tmp\/*\"\n ],\n emboss: [\n \"apt-get update -q\",\n \"apt-get install -y emboss\",\n \"apt-get clean -y\"\n ],\n fastagrep: [\n \"cd \/tmp\",\n \"wget http:\/\/bioinfo.ut.ee\/download\/dl.php?file=28 -O fastagrep.tar.gz\",\n \"tar -xzf fastagrep.tar.gz\",\n \"mv .\/fastagrep_v2.0_64bit_linux_2_6 \/opt\/biotools\/bin\/fastagrep\",\n \"rm -rf fastagrep.tar.gz\"\n ],\n },\n citations: {\n tlex3: [\n \"Mar\u00eda Bogaerts-M\u00e1rquez, Maite G Barr\u00f3n, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Ra\u00fal Castanera, Josep M Casacuberta, Josefa Gonz\u00e1lez, T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data, Bioinformatics, Volume 36, Issue 4, 15 February 2020, Pages 1191-1197, https:\/\/doi.org\/10.1093\/bioinformatics\/btz727\"\n ],\n RepeatMasker: [\n \"RepeatMasker. version Open 3.2.8 A.F.A. Smit, R. Hubley & P. Green RepeatMasker\"\n ],\n SHRIMP2: [\n \"David M, Dzamba M, Lister D, Ilie L, Brudno M. (2011) SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics. Apr 1;27(7):1011-2. Epub 2011 Jan 28.\"\n ],\n BLAT: [\n \"Kent W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res. 12:656-664\"\n ],\n samtools: [\n \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n ],\n bcftools: [\n \"Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509\"\n ],\n bwa: [\n \"Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324\"\n ],\n bwa-mem: [\n \"Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]\"\n ],\n }\n}\n" } ]