From 813eae892372f3fb3158a187912da474d039dc4c Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 6 Dec 2022 11:52:24 +0000 Subject: [PATCH 1/5] Manifests can point at local test-data folders now As of #149, each tool has its own test-data/ folder (currently a symlink to the top level shared folder). This means the manifest no longer needs to point at the top level folder. $ sed -i.bak "s#../../test-data/#test-data/#g" tools/*/.shed.yml --- tools/blast2go/.shed.yml | 4 +- tools/blast_rbh/.shed.yml | 26 +-- tools/blastxml_to_top_descr/.shed.yml | 8 +- tools/make_nr/.shed.yml | 14 +- tools/ncbi_blast_plus/.shed.yml | 228 +++++++++++++------------- 5 files changed, 140 insertions(+), 140 deletions(-) diff --git a/tools/blast2go/.shed.yml b/tools/blast2go/.shed.yml index 60522c21..eded482f 100644 --- a/tools/blast2go/.shed.yml +++ b/tools/blast2go/.shed.yml @@ -22,8 +22,8 @@ type: unrestricted include: - strip_components: 2 source: - - ../../test-data/blastp_sample.blast2go.tabular - - ../../test-data/blastp_sample.xml + - test-data/blastp_sample.blast2go.tabular + - test-data/blastp_sample.xml - ../../tool-data/blast2go.loc.sample - ../../tools/blast2go/README.rst - ../../tools/blast2go/blast2go.py diff --git a/tools/blast_rbh/.shed.yml b/tools/blast_rbh/.shed.yml index 0b841af7..297c9744 100644 --- a/tools/blast_rbh/.shed.yml +++ b/tools/blast_rbh/.shed.yml @@ -13,19 +13,19 @@ type: unrestricted include: - strip_components: 2 source: - - ../../test-data/four_human_proteins.fasta - - ../../test-data/k12_edited_proteins.fasta - - ../../test-data/k12_ten_proteins.fasta - - ../../test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular - - ../../test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular - - ../../test-data/rbh_blastp_k12.tabular - - ../../test-data/rbh_blastp_k12_self.tabular - - ../../test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular - - ../../test-data/rbh_none.tabular - - ../../test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular - - ../../test-data/rhodopsin_nucs.fasta - - ../../test-data/rhodopsin_proteins.fasta - - ../../test-data/three_human_mRNA.fasta + - test-data/four_human_proteins.fasta + - test-data/k12_edited_proteins.fasta + - test-data/k12_ten_proteins.fasta + - test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular + - test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular + - test-data/rbh_blastp_k12.tabular + - test-data/rbh_blastp_k12_self.tabular + - test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular + - test-data/rbh_none.tabular + - test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular + - test-data/rhodopsin_nucs.fasta + - test-data/rhodopsin_proteins.fasta + - test-data/three_human_mRNA.fasta - ../../tools/blast_rbh/README.rst - ../../tools/blast_rbh/best_hits.py - ../../tools/blast_rbh/blast_rbh.py diff --git a/tools/blastxml_to_top_descr/.shed.yml b/tools/blastxml_to_top_descr/.shed.yml index df6ebaf1..6dacf01c 100644 --- a/tools/blastxml_to_top_descr/.shed.yml +++ b/tools/blastxml_to_top_descr/.shed.yml @@ -27,10 +27,10 @@ type: unrestricted include: - strip_components: 2 source: - - ../../test-data/blastp_four_human_vs_rhodopsin.xml - - ../../test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin_top3.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular + - test-data/blastp_four_human_vs_rhodopsin.xml + - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular + - test-data/blastp_four_human_vs_rhodopsin_top3.tabular + - test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular - ../../tools/blastxml_to_top_descr/README.rst - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.py - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.xml diff --git a/tools/make_nr/.shed.yml b/tools/make_nr/.shed.yml index d0fc26a8..d95d4657 100644 --- a/tools/make_nr/.shed.yml +++ b/tools/make_nr/.shed.yml @@ -18,10 +18,10 @@ include: - ../../tools/make_nr/README.rst - ../../tools/make_nr/make_nr.py - ../../tools/make_nr/make_nr.xml - - ../../test-data/duplicates.fasta - - ../../test-data/duplicates.fasta.gz - - ../../test-data/duplicates.nr.fasta - - ../../test-data/more_duplicates.fasta - - ../../test-data/deduplicate.nosortids.fasta - - ../../test-data/deduplicate.sortids.fasta - - ../../test-data/empty.fasta + - test-data/duplicates.fasta + - test-data/duplicates.fasta.gz + - test-data/duplicates.nr.fasta + - test-data/more_duplicates.fasta + - test-data/deduplicate.nosortids.fasta + - test-data/deduplicate.sortids.fasta + - test-data/empty.fasta diff --git a/tools/ncbi_blast_plus/.shed.yml b/tools/ncbi_blast_plus/.shed.yml index f6900fd5..6f0ea8af 100644 --- a/tools/ncbi_blast_plus/.shed.yml +++ b/tools/ncbi_blast_plus/.shed.yml @@ -13,120 +13,120 @@ type: unrestricted include: - strip_components: 2 source: - - ../../test-data/blastdb.loc - - ../../test-data/blastdb_d.loc - - ../../test-data/blastdb_p.loc - - ../../test-data/blastn_arabidopsis.extended.tabular - - ../../test-data/blastn_arabidopsis.standard.tabular - - ../../test-data/blastn_arabidopsis.xml - - ../../test-data/blastn_chimera_vs_three_human_max1.tabular - - ../../test-data/blastn_chimera_vs_three_human_max1.txt - - ../../test-data/blastn_rhodopsin_vs_three_human.columns.tabular - - ../../test-data/blastn_rhodopsin_vs_three_human.tabular - - ../../test-data/blastn_rhodopsin_vs_three_human.xml - - ../../test-data/blastn_rhodopsin_vs_three_human_converted.tabular - - ../../test-data/blastn_chimera_vs_three_human_db.tabular - - ../../test-data/blastn_chimera_vs_rhodopsin_db.tabular - - ../../test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin.xml - - ../../test-data/blastp_four_human_vs_rhodopsin_converted.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular - - ../../test-data/blastp_four_human_vs_rhodopsin_ext.tabular - - ../../test-data/blastp_human_vs_pdb_seg_no.xml - - ../../test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular - - ../../test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular - - ../../test-data/blastp_rhodopsin_vs_four_human.tabular - - ../../test-data/blastp_sample.xml - - ../../test-data/blastp_sample_converted.tabular - - ../../test-data/blastx_rhodopsin_vs_four_human.tabular - - ../../test-data/blastx_rhodopsin_vs_four_human.xml - - ../../test-data/blastx_rhodopsin_vs_four_human_all.tabular - - ../../test-data/blastx_rhodopsin_vs_four_human_converted.tabular - - ../../test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular - - ../../test-data/blastx_rhodopsin_vs_four_human_ext.tabular - - ../../test-data/blastx_sample.xml - - ../../test-data/blastx_sample_converted.tabular - - ../../test-data/cd00003.smp - - ../../test-data/cd00003_and_cd00008.aux - - ../../test-data/cd00003_and_cd00008.freq - - ../../test-data/cd00003_and_cd00008.loo - - ../../test-data/cd00003_and_cd00008.phr - - ../../test-data/cd00003_and_cd00008.pin - - ../../test-data/cd00003_and_cd00008.psd - - ../../test-data/cd00003_and_cd00008.psi - - ../../test-data/cd00003_and_cd00008.psq - - ../../test-data/cd00003_and_cd00008.rps - - ../../test-data/cd00008.smp - - ../../test-data/chimera.fasta - - ../../test-data/chimera.fasta.gz - - ../../test-data/convert2blastmask_four_human_masked.maskinfo-asn1 - - ../../test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary - - ../../test-data/dustmasker_three_human.fasta - - ../../test-data/dustmasker_three_human.maskinfo-asn1 - - ../../test-data/dustmasker_three_human.maskinfo-asn1-binary - - ../../test-data/empty_file.dat - - ../../test-data/four_human_proteins.dbinfo.txt - - ../../test-data/four_human_proteins.fasta - - ../../test-data/four_human_proteins.fasta.log.txt - - ../../test-data/four_human_proteins.fasta.phd - - ../../test-data/four_human_proteins.fasta.phi - - ../../test-data/four_human_proteins.fasta.phr - - ../../test-data/four_human_proteins.fasta.pin - - ../../test-data/four_human_proteins.fasta.pog - - ../../test-data/four_human_proteins.fasta.psd - - ../../test-data/four_human_proteins.fasta.psi - - ../../test-data/four_human_proteins.fasta.psq - - ../../test-data/four_human_proteins_masked.fasta - - ../../test-data/four_human_proteins_taxid.fasta.log.txt - - ../../test-data/four_human_proteins_taxid.fasta.phd - - ../../test-data/four_human_proteins_taxid.fasta.phi - - ../../test-data/four_human_proteins_taxid.fasta.phr - - ../../test-data/four_human_proteins_taxid.fasta.pin - - ../../test-data/four_human_proteins_taxid.fasta.pog - - ../../test-data/four_human_proteins_taxid.fasta.psd - - ../../test-data/four_human_proteins_taxid.fasta.psi - - ../../test-data/four_human_proteins_taxid.fasta.psq - - ../../test-data/rhodopsin_nucs.dbinfo.txt - - ../../test-data/rhodopsin_nucs.fasta - - ../../test-data/rhodopsin_nucs.fasta.gz - - ../../test-data/rhodopsin_nucs.fasta.log.txt - - ../../test-data/rhodopsin_nucs.fasta.nhd - - ../../test-data/rhodopsin_nucs.fasta.nhi - - ../../test-data/rhodopsin_nucs.fasta.nhr - - ../../test-data/rhodopsin_nucs.fasta.nin - - ../../test-data/rhodopsin_nucs.fasta.nog - - ../../test-data/rhodopsin_nucs.fasta.nsd - - ../../test-data/rhodopsin_nucs.fasta.nsi - - ../../test-data/rhodopsin_nucs.fasta.nsq - - ../../test-data/rhodopsin_nucs.fasta.nnd - - ../../test-data/rhodopsin_nucs.fasta.nni - - ../../test-data/rhodopsin_nucs.no_gi.fasta - - ../../test-data/rhodopsin_nucs.blastdbcmd.txt - - ../../test-data/rhodopsin_bufo.fasta - - ../../test-data/rhodopsin_proteins.fasta - - ../../test-data/segmasker_four_human.fasta - - ../../test-data/segmasker_four_human.maskinfo-asn1 - - ../../test-data/segmasker_four_human.maskinfo-asn1-binary - - ../../test-data/tblastn_four_human_vs_rhodopsin.html - - ../../test-data/tblastn_four_human_vs_rhodopsin.tabular - - ../../test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular - - ../../test-data/tblastn_four_human_vs_rhodopsin.xml - - ../../test-data/tblastn_four_human_vs_rhodopsin_ext.tabular - - ../../test-data/tblastx_rhodopsin_vs_three_human.tabular - - ../../test-data/three_human_mRNA.dbinfo.txt - - ../../test-data/three_human_mRNA.fasta - - ../../test-data/three_human_mRNA.fasta.gz - - ../../test-data/three_human_mRNA.fasta.log.txt - - ../../test-data/three_human_mRNA.fasta.nhd - - ../../test-data/three_human_mRNA.fasta.nhi - - ../../test-data/three_human_mRNA.fasta.nhr - - ../../test-data/three_human_mRNA.fasta.nin - - ../../test-data/three_human_mRNA.fasta.nog - - ../../test-data/three_human_mRNA.fasta.nsd - - ../../test-data/three_human_mRNA.fasta.nsi - - ../../test-data/three_human_mRNA.fasta.nsq - - ../../test-data/tool_data_table_conf.xml.test + - test-data/blastdb.loc + - test-data/blastdb_d.loc + - test-data/blastdb_p.loc + - test-data/blastn_arabidopsis.extended.tabular + - test-data/blastn_arabidopsis.standard.tabular + - test-data/blastn_arabidopsis.xml + - test-data/blastn_chimera_vs_three_human_max1.tabular + - test-data/blastn_chimera_vs_three_human_max1.txt + - test-data/blastn_rhodopsin_vs_three_human.columns.tabular + - test-data/blastn_rhodopsin_vs_three_human.tabular + - test-data/blastn_rhodopsin_vs_three_human.xml + - test-data/blastn_rhodopsin_vs_three_human_converted.tabular + - test-data/blastn_chimera_vs_three_human_db.tabular + - test-data/blastn_chimera_vs_rhodopsin_db.tabular + - test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular + - test-data/blastp_four_human_vs_rhodopsin.tabular + - test-data/blastp_four_human_vs_rhodopsin.xml + - test-data/blastp_four_human_vs_rhodopsin_converted.tabular + - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular + - test-data/blastp_four_human_vs_rhodopsin_ext.tabular + - test-data/blastp_human_vs_pdb_seg_no.xml + - test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular + - test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular + - test-data/blastp_rhodopsin_vs_four_human.tabular + - test-data/blastp_sample.xml + - test-data/blastp_sample_converted.tabular + - test-data/blastx_rhodopsin_vs_four_human.tabular + - test-data/blastx_rhodopsin_vs_four_human.xml + - test-data/blastx_rhodopsin_vs_four_human_all.tabular + - test-data/blastx_rhodopsin_vs_four_human_converted.tabular + - test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular + - test-data/blastx_rhodopsin_vs_four_human_ext.tabular + - test-data/blastx_sample.xml + - test-data/blastx_sample_converted.tabular + - test-data/cd00003.smp + - test-data/cd00003_and_cd00008.aux + - test-data/cd00003_and_cd00008.freq + - test-data/cd00003_and_cd00008.loo + - test-data/cd00003_and_cd00008.phr + - test-data/cd00003_and_cd00008.pin + - test-data/cd00003_and_cd00008.psd + - test-data/cd00003_and_cd00008.psi + - test-data/cd00003_and_cd00008.psq + - test-data/cd00003_and_cd00008.rps + - test-data/cd00008.smp + - test-data/chimera.fasta + - test-data/chimera.fasta.gz + - test-data/convert2blastmask_four_human_masked.maskinfo-asn1 + - test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary + - test-data/dustmasker_three_human.fasta + - test-data/dustmasker_three_human.maskinfo-asn1 + - test-data/dustmasker_three_human.maskinfo-asn1-binary + - test-data/empty_file.dat + - test-data/four_human_proteins.dbinfo.txt + - test-data/four_human_proteins.fasta + - test-data/four_human_proteins.fasta.log.txt + - test-data/four_human_proteins.fasta.phd + - test-data/four_human_proteins.fasta.phi + - test-data/four_human_proteins.fasta.phr + - test-data/four_human_proteins.fasta.pin + - test-data/four_human_proteins.fasta.pog + - test-data/four_human_proteins.fasta.psd + - test-data/four_human_proteins.fasta.psi + - test-data/four_human_proteins.fasta.psq + - test-data/four_human_proteins_masked.fasta + - test-data/four_human_proteins_taxid.fasta.log.txt + - test-data/four_human_proteins_taxid.fasta.phd + - test-data/four_human_proteins_taxid.fasta.phi + - test-data/four_human_proteins_taxid.fasta.phr + - test-data/four_human_proteins_taxid.fasta.pin + - test-data/four_human_proteins_taxid.fasta.pog + - test-data/four_human_proteins_taxid.fasta.psd + - test-data/four_human_proteins_taxid.fasta.psi + - test-data/four_human_proteins_taxid.fasta.psq + - test-data/rhodopsin_nucs.dbinfo.txt + - test-data/rhodopsin_nucs.fasta + - test-data/rhodopsin_nucs.fasta.gz + - test-data/rhodopsin_nucs.fasta.log.txt + - test-data/rhodopsin_nucs.fasta.nhd + - test-data/rhodopsin_nucs.fasta.nhi + - test-data/rhodopsin_nucs.fasta.nhr + - test-data/rhodopsin_nucs.fasta.nin + - test-data/rhodopsin_nucs.fasta.nog + - test-data/rhodopsin_nucs.fasta.nsd + - test-data/rhodopsin_nucs.fasta.nsi + - test-data/rhodopsin_nucs.fasta.nsq + - test-data/rhodopsin_nucs.fasta.nnd + - test-data/rhodopsin_nucs.fasta.nni + - test-data/rhodopsin_nucs.no_gi.fasta + - test-data/rhodopsin_nucs.blastdbcmd.txt + - test-data/rhodopsin_bufo.fasta + - test-data/rhodopsin_proteins.fasta + - test-data/segmasker_four_human.fasta + - test-data/segmasker_four_human.maskinfo-asn1 + - test-data/segmasker_four_human.maskinfo-asn1-binary + - test-data/tblastn_four_human_vs_rhodopsin.html + - test-data/tblastn_four_human_vs_rhodopsin.tabular + - test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular + - test-data/tblastn_four_human_vs_rhodopsin.xml + - test-data/tblastn_four_human_vs_rhodopsin_ext.tabular + - test-data/tblastx_rhodopsin_vs_three_human.tabular + - test-data/three_human_mRNA.dbinfo.txt + - test-data/three_human_mRNA.fasta + - test-data/three_human_mRNA.fasta.gz + - test-data/three_human_mRNA.fasta.log.txt + - test-data/three_human_mRNA.fasta.nhd + - test-data/three_human_mRNA.fasta.nhi + - test-data/three_human_mRNA.fasta.nhr + - test-data/three_human_mRNA.fasta.nin + - test-data/three_human_mRNA.fasta.nog + - test-data/three_human_mRNA.fasta.nsd + - test-data/three_human_mRNA.fasta.nsi + - test-data/three_human_mRNA.fasta.nsq + - test-data/tool_data_table_conf.xml.test - ../../tool-data/blastdb.loc.sample - ../../tool-data/blastdb_d.loc.sample - ../../tool-data/blastdb_p.loc.sample From d8a91ca3a11a36afa6ba1a52dcdd5ea0f68af03b Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 6 Dec 2022 11:57:41 +0000 Subject: [PATCH 2/5] No need for relative path to local files This was sensible for consistency with the top-level shared tool-data and test-data folders, but we're phasing that out to follow IUC standard layout --- tools/blast2go/.shed.yml | 8 +++--- tools/blast_rbh/.shed.yml | 8 +++--- tools/blastxml_to_top_descr/.shed.yml | 6 ++-- tools/make_nr/.shed.yml | 6 ++-- tools/ncbi_blast_plus/.shed.yml | 40 +++++++++++++-------------- 5 files changed, 34 insertions(+), 34 deletions(-) diff --git a/tools/blast2go/.shed.yml b/tools/blast2go/.shed.yml index eded482f..be32127d 100644 --- a/tools/blast2go/.shed.yml +++ b/tools/blast2go/.shed.yml @@ -25,7 +25,7 @@ include: - test-data/blastp_sample.blast2go.tabular - test-data/blastp_sample.xml - ../../tool-data/blast2go.loc.sample - - ../../tools/blast2go/README.rst - - ../../tools/blast2go/blast2go.py - - ../../tools/blast2go/blast2go.xml - - ../../tools/blast2go/massage_xml_for_blast2go.py + - README.rst + - blast2go.py + - blast2go.xml + - massage_xml_for_blast2go.py diff --git a/tools/blast_rbh/.shed.yml b/tools/blast_rbh/.shed.yml index 297c9744..a974f321 100644 --- a/tools/blast_rbh/.shed.yml +++ b/tools/blast_rbh/.shed.yml @@ -26,7 +26,7 @@ include: - test-data/rhodopsin_nucs.fasta - test-data/rhodopsin_proteins.fasta - test-data/three_human_mRNA.fasta - - ../../tools/blast_rbh/README.rst - - ../../tools/blast_rbh/best_hits.py - - ../../tools/blast_rbh/blast_rbh.py - - ../../tools/blast_rbh/blast_rbh.xml + - README.rst + - best_hits.py + - blast_rbh.py + - blast_rbh.xml diff --git a/tools/blastxml_to_top_descr/.shed.yml b/tools/blastxml_to_top_descr/.shed.yml index 6dacf01c..79e0ddc1 100644 --- a/tools/blastxml_to_top_descr/.shed.yml +++ b/tools/blastxml_to_top_descr/.shed.yml @@ -31,6 +31,6 @@ include: - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular - test-data/blastp_four_human_vs_rhodopsin_top3.tabular - test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular - - ../../tools/blastxml_to_top_descr/README.rst - - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.py - - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.xml + - README.rst + - blastxml_to_top_descr.py + - blastxml_to_top_descr.xml diff --git a/tools/make_nr/.shed.yml b/tools/make_nr/.shed.yml index d95d4657..964f75d8 100644 --- a/tools/make_nr/.shed.yml +++ b/tools/make_nr/.shed.yml @@ -15,9 +15,9 @@ type: unrestricted include: - strip_components: 2 source: - - ../../tools/make_nr/README.rst - - ../../tools/make_nr/make_nr.py - - ../../tools/make_nr/make_nr.xml + - README.rst + - make_nr.py + - make_nr.xml - test-data/duplicates.fasta - test-data/duplicates.fasta.gz - test-data/duplicates.nr.fasta diff --git a/tools/ncbi_blast_plus/.shed.yml b/tools/ncbi_blast_plus/.shed.yml index 6f0ea8af..12b3501f 100644 --- a/tools/ncbi_blast_plus/.shed.yml +++ b/tools/ncbi_blast_plus/.shed.yml @@ -131,23 +131,23 @@ include: - ../../tool-data/blastdb_d.loc.sample - ../../tool-data/blastdb_p.loc.sample - ../../tool-data/tool_data_table_conf.xml.sample - - ../../tools/ncbi_blast_plus/get_species_taxids.xml - - ../../tools/ncbi_blast_plus/README.rst - - ../../tools/ncbi_blast_plus/blastxml_to_tabular.py - - ../../tools/ncbi_blast_plus/blastxml_to_tabular.xml - - ../../tools/ncbi_blast_plus/check_no_duplicates.py - - ../../tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml - - ../../tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_macros.xml - - ../../tools/ncbi_blast_plus/ncbi_makeblastdb.xml - - ../../tools/ncbi_blast_plus/ncbi_makeprofiledb.xml - - ../../tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml - - ../../tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml + - get_species_taxids.xml + - README.rst + - blastxml_to_tabular.py + - blastxml_to_tabular.xml + - check_no_duplicates.py + - ncbi_blastdbcmd_info.xml + - ncbi_blastdbcmd_wrapper.xml + - ncbi_blastn_wrapper.xml + - ncbi_blastp_wrapper.xml + - ncbi_blastx_wrapper.xml + - ncbi_convert2blastmask_wrapper.xml + - ncbi_dustmasker_wrapper.xml + - ncbi_macros.xml + - ncbi_makeblastdb.xml + - ncbi_makeprofiledb.xml + - ncbi_rpsblast_wrapper.xml + - ncbi_rpstblastn_wrapper.xml + - ncbi_segmasker_wrapper.xml + - ncbi_tblastn_wrapper.xml + - ncbi_tblastx_wrapper.xml From 960eecdc7a0d9ab3dfbd5daf56d29de210cb56be Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 6 Dec 2022 12:02:50 +0000 Subject: [PATCH 3/5] Breakup top-level tool-data folder Now using per-tool sub-folders as per IUC recommended layout. --- .../tool-data}/tool_data_table_conf.xml.sample | 0 tool-data/README.rst | 9 --------- tools/blast2go/.shed.yml | 2 +- .../blast2go/tool-data}/blast2go.loc.sample | 0 tools/ncbi_blast_plus/.shed.yml | 8 ++++---- tools/ncbi_blast_plus/tool-data | 1 - .../ncbi_blast_plus/tool-data}/blastdb.loc.sample | 0 .../ncbi_blast_plus/tool-data}/blastdb_d.loc.sample | 0 .../ncbi_blast_plus/tool-data}/blastdb_p.loc.sample | 0 9 files changed, 5 insertions(+), 15 deletions(-) rename {tool-data => datatypes/blast_datatypes/tool-data}/tool_data_table_conf.xml.sample (100%) delete mode 100644 tool-data/README.rst rename {tool-data => tools/blast2go/tool-data}/blast2go.loc.sample (100%) delete mode 120000 tools/ncbi_blast_plus/tool-data rename {tool-data => tools/ncbi_blast_plus/tool-data}/blastdb.loc.sample (100%) rename {tool-data => tools/ncbi_blast_plus/tool-data}/blastdb_d.loc.sample (100%) rename {tool-data => tools/ncbi_blast_plus/tool-data}/blastdb_p.loc.sample (100%) diff --git a/tool-data/tool_data_table_conf.xml.sample b/datatypes/blast_datatypes/tool-data/tool_data_table_conf.xml.sample similarity index 100% rename from tool-data/tool_data_table_conf.xml.sample rename to datatypes/blast_datatypes/tool-data/tool_data_table_conf.xml.sample diff --git a/tool-data/README.rst b/tool-data/README.rst deleted file mode 100644 index 789c0e71..00000000 --- a/tool-data/README.rst +++ /dev/null @@ -1,9 +0,0 @@ -Galaxy Tool sample data -======================= - -This folder contains sample files used by Galaxy tools defined elsewhere -in this repository. For example, ``blastdb_p.loc.sample`` is a sample -file used to generate the default ``blastdb_p.loc`` file describing any -system-level protein BLAST databases available within Galaxy. - -For general information, see the `main README file <../README.rst>`_. diff --git a/tools/blast2go/.shed.yml b/tools/blast2go/.shed.yml index be32127d..81ff3808 100644 --- a/tools/blast2go/.shed.yml +++ b/tools/blast2go/.shed.yml @@ -24,7 +24,7 @@ include: source: - test-data/blastp_sample.blast2go.tabular - test-data/blastp_sample.xml - - ../../tool-data/blast2go.loc.sample + - tool-data/blast2go.loc.sample - README.rst - blast2go.py - blast2go.xml diff --git a/tool-data/blast2go.loc.sample b/tools/blast2go/tool-data/blast2go.loc.sample similarity index 100% rename from tool-data/blast2go.loc.sample rename to tools/blast2go/tool-data/blast2go.loc.sample diff --git a/tools/ncbi_blast_plus/.shed.yml b/tools/ncbi_blast_plus/.shed.yml index 12b3501f..fefb27bf 100644 --- a/tools/ncbi_blast_plus/.shed.yml +++ b/tools/ncbi_blast_plus/.shed.yml @@ -127,10 +127,10 @@ include: - test-data/three_human_mRNA.fasta.nsi - test-data/three_human_mRNA.fasta.nsq - test-data/tool_data_table_conf.xml.test - - ../../tool-data/blastdb.loc.sample - - ../../tool-data/blastdb_d.loc.sample - - ../../tool-data/blastdb_p.loc.sample - - ../../tool-data/tool_data_table_conf.xml.sample + - tool-data/blastdb.loc.sample + - tool-data/blastdb_d.loc.sample + - tool-data/blastdb_p.loc.sample + - tool-data/tool_data_table_conf.xml.sample - get_species_taxids.xml - README.rst - blastxml_to_tabular.py diff --git a/tools/ncbi_blast_plus/tool-data b/tools/ncbi_blast_plus/tool-data deleted file mode 120000 index 4103a678..00000000 --- a/tools/ncbi_blast_plus/tool-data +++ /dev/null @@ -1 +0,0 @@ -../../tool-data \ No newline at end of file diff --git a/tool-data/blastdb.loc.sample b/tools/ncbi_blast_plus/tool-data/blastdb.loc.sample similarity index 100% rename from tool-data/blastdb.loc.sample rename to tools/ncbi_blast_plus/tool-data/blastdb.loc.sample diff --git a/tool-data/blastdb_d.loc.sample b/tools/ncbi_blast_plus/tool-data/blastdb_d.loc.sample similarity index 100% rename from tool-data/blastdb_d.loc.sample rename to tools/ncbi_blast_plus/tool-data/blastdb_d.loc.sample diff --git a/tool-data/blastdb_p.loc.sample b/tools/ncbi_blast_plus/tool-data/blastdb_p.loc.sample similarity index 100% rename from tool-data/blastdb_p.loc.sample rename to tools/ncbi_blast_plus/tool-data/blastdb_p.loc.sample From 2a4c00a545c78a1c5ca303b05cbe035057d66f78 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 6 Dec 2022 13:45:19 +0000 Subject: [PATCH 4/5] Update README about test-data and tool-data folders --- README.rst | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index f26d0443..b3e83db7 100644 --- a/README.rst +++ b/README.rst @@ -136,11 +136,10 @@ datatype definitions (obsolete), and ``data_managers`` contains Galaxy Data Managers for tasks like setting up local copies of NCBI BLAST databases (currently unfinished). -All of these child folders contain additional README files, which cover -things like how to install each tool manually or via the Galaxy Tool Shed. - -Additionally there is a shared ``test-data`` folder used for functional test -sample data, and a shared ``tool-data`` folder used for configuration files. +All of these child folders contain additional README files, which cover things +like how to install each tool manually or via the Galaxy Tool Shed, subfolder +``test-data`` for functional test sample data, and sometimes a subfolder +``tool-data`` for configuration files. Installation From 0f09fcc802c3dba985360478d794866fbc7c5aea Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 6 Dec 2022 14:37:45 +0000 Subject: [PATCH 5/5] No longer need strip_components: 2 for manifests --- tools/blast2go/.shed.yml | 2 +- tools/blast_rbh/.shed.yml | 2 +- tools/blastxml_to_top_descr/.shed.yml | 2 +- tools/make_nr/.shed.yml | 2 +- tools/ncbi_blast_plus/.shed.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/tools/blast2go/.shed.yml b/tools/blast2go/.shed.yml index 81ff3808..5d26e5d2 100644 --- a/tools/blast2go/.shed.yml +++ b/tools/blast2go/.shed.yml @@ -20,7 +20,7 @@ categories: - Sequence Analysis type: unrestricted include: -- strip_components: 2 +- strip_components: 0 source: - test-data/blastp_sample.blast2go.tabular - test-data/blastp_sample.xml diff --git a/tools/blast_rbh/.shed.yml b/tools/blast_rbh/.shed.yml index a974f321..e29744db 100644 --- a/tools/blast_rbh/.shed.yml +++ b/tools/blast_rbh/.shed.yml @@ -11,7 +11,7 @@ categories: - Sequence Analysis type: unrestricted include: -- strip_components: 2 +- strip_components: 0 source: - test-data/four_human_proteins.fasta - test-data/k12_edited_proteins.fasta diff --git a/tools/blastxml_to_top_descr/.shed.yml b/tools/blastxml_to_top_descr/.shed.yml index 79e0ddc1..ed09d869 100644 --- a/tools/blastxml_to_top_descr/.shed.yml +++ b/tools/blastxml_to_top_descr/.shed.yml @@ -25,7 +25,7 @@ categories: - Text Manipulation type: unrestricted include: -- strip_components: 2 +- strip_components: 0 source: - test-data/blastp_four_human_vs_rhodopsin.xml - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular diff --git a/tools/make_nr/.shed.yml b/tools/make_nr/.shed.yml index 964f75d8..98ae8c5b 100644 --- a/tools/make_nr/.shed.yml +++ b/tools/make_nr/.shed.yml @@ -13,7 +13,7 @@ categories: - Sequence Analysis type: unrestricted include: -- strip_components: 2 +- strip_components: 0 source: - README.rst - make_nr.py diff --git a/tools/ncbi_blast_plus/.shed.yml b/tools/ncbi_blast_plus/.shed.yml index fefb27bf..eee04802 100644 --- a/tools/ncbi_blast_plus/.shed.yml +++ b/tools/ncbi_blast_plus/.shed.yml @@ -11,7 +11,7 @@ categories: - Sequence Analysis type: unrestricted include: -- strip_components: 2 +- strip_components: 0 source: - test-data/blastdb.loc - test-data/blastdb_d.loc