From 3805fa13e52bf2c9c8c314fb0675c5407cf16718 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 15 Mar 2025 18:16:50 +0100 Subject: [PATCH] repeatmasker: bump and dfam data table Repeatmasker (in containers) is broken since version 4.1.5 build 1 since the [download of the repeat libraries has been removed](https://github.com/bioconda/bioconda-recipes/pull/43288) ([see also](https://github.com/bioconda/bioconda-recipes/pull/45513)). This provides dfam data via a data table --- tools/repeatmasker/.lint_skip | 3 - tools/repeatmasker/macros.xml | 2 +- tools/repeatmasker/repeatmasker.xml | 89 ++++++++++++------- tools/repeatmasker/test-data/small.fasta.cat | 4 +- .../repeatmasker/test-data/small.fasta.stats | 8 +- .../test-data/small_dfam.fasta.cat | 22 +---- .../test-data/small_dfam.fasta.log | 5 +- .../test-data/small_dfam.fasta.masked | 6 +- .../test-data/small_dfam.fasta.stats | 18 ++-- .../test-data/small_dfam_rattus.fasta.cat | 6 +- .../test-data/small_dfam_rattus.fasta.stats | 10 +-- .../test-data/small_dfam_up.fasta.cat | 6 +- .../test-data/small_dfam_up.fasta.stats | 8 +- 13 files changed, 98 insertions(+), 89 deletions(-) delete mode 100644 tools/repeatmasker/.lint_skip diff --git a/tools/repeatmasker/.lint_skip b/tools/repeatmasker/.lint_skip deleted file mode 100644 index dd77e7a23b8..00000000000 --- a/tools/repeatmasker/.lint_skip +++ /dev/null @@ -1,3 +0,0 @@ -InputsNameRedundantArgument -XMLOrder -TestsCaseValidation diff --git a/tools/repeatmasker/macros.xml b/tools/repeatmasker/macros.xml index f32cdf9cc1b..090f4ba6ab6 100644 --- a/tools/repeatmasker/macros.xml +++ b/tools/repeatmasker/macros.xml @@ -1,5 +1,5 @@ - 4.1.5 + 4.1.7 galaxy0 diff --git a/tools/repeatmasker/repeatmasker.xml b/tools/repeatmasker/repeatmasker.xml index 29796e2adae..de7f8c433c5 100644 --- a/tools/repeatmasker/repeatmasker.xml +++ b/tools/repeatmasker/repeatmasker.xml @@ -3,8 +3,8 @@ macros.xml - + repeatmasker --version &2 ; exit 1 ; fi && if [ -z "\$RM_LIB_PATH" ] ; then RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries ; fi && - #if $repeat_source.source_type == "dfam_up": - mkdir lib/ && - ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 && - RM_LIB_PATH=\$(pwd)/lib && + + mkdir RM_LIB_PATH && + for l in \$RM_LIB_PATH/*; + do + ln -s "\$l" RM_LIB_PATH/"\$(basename \$l)"; + done && + + #if $repeat_source.source_type == "dfam": + ln -fs '${repeat_source.dfam_lib.fields.path}' RM_LIB_PATH/RepeatMaskerLib.h5 && + #elif $repeat_source.source_type == "dfam_up": + ln -fs '${repeat_source.dfam_lib}' RM_LIB_PATH/RepeatMaskerLib.h5 && #end if ln -s '${input_fasta}' rm_input.fasta && RepeatMasker -dir \$(pwd) - -libdir \$RM_LIB_PATH + -libdir RM_LIB_PATH #if $repeat_source.source_type == "library": -lib '${repeat_source.repeat_lib}' -cutoff '${repeat_source.cutoff}' #else if $repeat_source.source_type == "dfam": #if $repeat_source.species_source.species_from_list == 'yes': - -species $repeat_source.species_source.species_list + -species '$repeat_source.species_source.species_list' #else -species '${repeat_source.species_source.species_name}' #end if @@ -92,6 +99,10 @@ + + + + @@ -99,27 +110,27 @@ - + - - - - - + + + + + - + - + - + @@ -178,8 +189,10 @@ - - + + + + @@ -187,11 +200,15 @@ - - - - - + + + + + +
+ + +
@@ -202,8 +219,13 @@ - - + + + + + + + @@ -211,9 +233,11 @@ - - - + + + + + @@ -221,8 +245,13 @@ - - + + + + + + + diff --git a/tools/repeatmasker/test-data/small.fasta.cat b/tools/repeatmasker/test-data/small.fasta.cat index 27a707e50db..ec2a506ed04 100644 --- a/tools/repeatmasker/test-data/small.fasta.cat +++ b/tools/repeatmasker/test-data/small.fasta.cat @@ -98,6 +98,6 @@ Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.5 , default mode -run with rmblastn version 2.13.0+ +RepeatMasker version 4.1.7-p1 , default mode +run with rmblastn version 2.14.1+ RM Library: diff --git a/tools/repeatmasker/test-data/small.fasta.stats b/tools/repeatmasker/test-data/small.fasta.stats index 8301fa44462..bc94a60b3c0 100644 --- a/tools/repeatmasker/test-data/small.fasta.stats +++ b/tools/repeatmasker/test-data/small.fasta.stats @@ -53,8 +53,8 @@ Low complexity: 0 0 bp 0.00 % Runs of >=20 X/Ns in query were excluded in % calcs -RepeatMasker version 4.1.5 , default mode - -run with rmblastn version 2.13.0+ -The query was compared to unclassified sequences in ".../dataset_9e3ddbd2-0776-4c6d-bed6-0f4cd415796c.dat" +RepeatMasker version 4.1.7-p1 , default mode + +run with rmblastn version 2.14.1+ +The query was compared to unclassified sequences in ".../dataset_37f353be-1b0e-4054-b3c1-b0b207477de3.dat" FamDB: diff --git a/tools/repeatmasker/test-data/small_dfam.fasta.cat b/tools/repeatmasker/test-data/small_dfam.fasta.cat index 90b2ad07bbf..0f5de93bcc2 100644 --- a/tools/repeatmasker/test-data/small_dfam.fasta.cat +++ b/tools/repeatmasker/test-data/small_dfam.fasta.cat @@ -70,22 +70,6 @@ Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) -180 25.44 1.41 5.88 scaffold_1 8140 8210 (5941) C AmnL2-1#LINE/L2 (11) 2602 2535 m_b1s601i0 - - scaffold_1 8140 ACAACATTATTTTGTCTA-CACCCTGCATACAGCACAGTATATTAAATTT 8188 - v v - ii i v i- v vii --- -C AmnL2-1#LINE/ 2602 ACAACTTTATTTTGTATAGCGTCTTTCATACAA-ACTGTATCCCAAA--- 2557 - - scaffold_1 8189 AGGTTTTATTAAGTTAAGTAAT 8210 - v i ivi i -C AmnL2-1#LINE/ 2556 ACGCTTTACAGAGTTAAATAAT 2535 - -Matrix = 25p39g.matrix -Kimura (with divCpGMod) = 29.45 -CpG sites = 10, Kimura (unadjusted) = 31.65 -Transitions / transversions = 1.43 (10/7) -Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) - 67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 @@ -114,6 +98,6 @@ Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.5 , default mode -run with rmblastn version 2.13.0+ -RM Library: CONS-Dfam_3.7 +RepeatMasker version 4.1.7-p1 , default mode +run with rmblastn version 2.14.1+ +RM Library: CONS-Dfam_3.8 diff --git a/tools/repeatmasker/test-data/small_dfam.fasta.log b/tools/repeatmasker/test-data/small_dfam.fasta.log index fc18e387ac9..0b437f356df 100644 --- a/tools/repeatmasker/test-data/small_dfam.fasta.log +++ b/tools/repeatmasker/test-data/small_dfam.fasta.log @@ -6,6 +6,5 @@ SW score % div. % del. % ins. query sequence pos in query: begin end (left) rep 15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 -180 25.4 1.4 5.9 scaffold_1 8140 8210 (6010) C AmnL2-1 LINE/L2 (11) 2602 2535 7 -67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 8 -19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 8 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 7 diff --git a/tools/repeatmasker/test-data/small_dfam.fasta.masked b/tools/repeatmasker/test-data/small_dfam.fasta.masked index da1df186866..a8559cea671 100644 --- a/tools/repeatmasker/test-data/small_dfam.fasta.masked +++ b/tools/repeatmasker/test-data/small_dfam.fasta.masked @@ -161,9 +161,9 @@ TGTACACTTACTTCTATGGAAAAGATGGAGCGCCACAGTGAAAACTGTTT TGAGTCTGTGAGGGGAAAACACAGCATCAGTCACAGTGAAACACTAGGTG GCACTCAGGTTTGACATTCAAGCATTTGTATCCCACAGTTACTGTTGCTG GGTTGTTGGCTGGCATGCAACTTAATATGATCTATCTTTAAATCAGTGTG -TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCNNNNNNNNNNN -NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -NNNNNNNNNNGTTCTGAGGTGGCATTGCCCTCAGGTATATATCCCTCAGG +TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCACAACATTATT +TTGTCTACACCCTGCATACAGCACAGTATATTAAATTTAGGTTTTATTAA +GTTAAGTAATGTTCTGAGGTGGCATTGCCCTCAGGTATATATCCCTCAGG CAGTGTTACTGGACAGCATATAGATTGTAATGTTGTGTAAGCAGTGTTGT GTAAGCTTTTTTAACCAAAATGCTCTCATGTTTCTTTGTTACCACAGTGG TTTTAGTGATGTTTTGTGCTGTGAACAGAATCATGATTTCTGCAGACACT diff --git a/tools/repeatmasker/test-data/small_dfam.fasta.stats b/tools/repeatmasker/test-data/small_dfam.fasta.stats index 052511d6584..dce5aae6c60 100644 --- a/tools/repeatmasker/test-data/small_dfam.fasta.stats +++ b/tools/repeatmasker/test-data/small_dfam.fasta.stats @@ -3,7 +3,7 @@ file name: rm_input.fasta sequences: 1 total length: 14220 bp (14220 bp excl N/X-runs) GC level: 39.94 % -bases masked: 449 bp ( 3.16 %) +bases masked: 378 bp ( 2.66 %) ================================================== number of length percentage elements* occupied of sequence @@ -12,9 +12,9 @@ SINEs: 0 0 bp 0.00 % ALUs 0 0 bp 0.00 % MIRs 0 0 bp 0.00 % -LINEs: 1 71 bp 0.50 % +LINEs: 0 0 bp 0.00 % LINE1 0 0 bp 0.00 % - LINE2 1 71 bp 0.50 % + LINE2 0 0 bp 0.00 % L3/CR1 0 0 bp 0.00 % LTR elements: 0 0 bp 0.00 % @@ -29,7 +29,7 @@ DNA elements: 0 0 bp 0.00 % Unclassified: 0 0 bp 0.00 % -Total interspersed repeats: 71 bp 0.50 % +Total interspersed repeats: 0 bp 0.00 % Small RNA: 0 0 bp 0.00 % @@ -44,8 +44,8 @@ Low complexity: 0 0 bp 0.00 % Runs of >=20 X/Ns in query were excluded in % calcs -The query species was assumed to be human -RepeatMasker version 4.1.5 , default mode - -run with rmblastn version 2.13.0+ -FamDB: CONS-Dfam_3.7 +The query species was assumed to be Homo sapiens +RepeatMasker version 4.1.7-p1 , default mode + +run with rmblastn version 2.14.1+ +FamDB: CONS-Dfam_3.8 diff --git a/tools/repeatmasker/test-data/small_dfam_rattus.fasta.cat b/tools/repeatmasker/test-data/small_dfam_rattus.fasta.cat index 0b58d22fff5..0f5de93bcc2 100644 --- a/tools/repeatmasker/test-data/small_dfam_rattus.fasta.cat +++ b/tools/repeatmasker/test-data/small_dfam_rattus.fasta.cat @@ -98,6 +98,6 @@ Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.5 , default mode -run with rmblastn version 2.13.0+ -RM Library: CONS-Dfam_3.7 +RepeatMasker version 4.1.7-p1 , default mode +run with rmblastn version 2.14.1+ +RM Library: CONS-Dfam_3.8 diff --git a/tools/repeatmasker/test-data/small_dfam_rattus.fasta.stats b/tools/repeatmasker/test-data/small_dfam_rattus.fasta.stats index 712fff6fe4d..974cd4f92f7 100644 --- a/tools/repeatmasker/test-data/small_dfam_rattus.fasta.stats +++ b/tools/repeatmasker/test-data/small_dfam_rattus.fasta.stats @@ -47,8 +47,8 @@ Low complexity: 0 0 bp 0.00 % Runs of >=20 X/Ns in query were excluded in % calcs -The query species was assumed to be rattus -RepeatMasker version 4.1.5 , default mode - -run with rmblastn version 2.13.0+ -FamDB: CONS-Dfam_3.7 +The query species was assumed to be rodent +RepeatMasker version 4.1.7-p1 , default mode + +run with rmblastn version 2.14.1+ +FamDB: CONS-Dfam_3.8 diff --git a/tools/repeatmasker/test-data/small_dfam_up.fasta.cat b/tools/repeatmasker/test-data/small_dfam_up.fasta.cat index 6c09a24b667..0f5de93bcc2 100644 --- a/tools/repeatmasker/test-data/small_dfam_up.fasta.cat +++ b/tools/repeatmasker/test-data/small_dfam_up.fasta.cat @@ -98,6 +98,6 @@ Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.5 , default mode -run with rmblastn version 2.13.0+ -RM Library: CONS-Dfam_1.0 +RepeatMasker version 4.1.7-p1 , default mode +run with rmblastn version 2.14.1+ +RM Library: CONS-Dfam_3.8 diff --git a/tools/repeatmasker/test-data/small_dfam_up.fasta.stats b/tools/repeatmasker/test-data/small_dfam_up.fasta.stats index 7a18633d906..974cd4f92f7 100644 --- a/tools/repeatmasker/test-data/small_dfam_up.fasta.stats +++ b/tools/repeatmasker/test-data/small_dfam_up.fasta.stats @@ -48,7 +48,7 @@ Low complexity: 0 0 bp 0.00 % The query species was assumed to be rodent -RepeatMasker version 4.1.5 , default mode - -run with rmblastn version 2.13.0+ -FamDB: CONS-Dfam_1.0 +RepeatMasker version 4.1.7-p1 , default mode + +run with rmblastn version 2.14.1+ +FamDB: CONS-Dfam_3.8