Problem with Ragout installed from Bioconda: ERROR: "ragout-maf2synteny" native module not found

[amizeranschi]

Hi,

I've installed Ragout from Bioconda into a new environment (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/ragout/meta.yaml)

$ ragout.py --version
2.0

and I'm getting an error while running Ragout on Cactus's evolverMammals example (https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt):

echo ".references = simRat_chr6,simCow_chr6,simDog_chr6,simHuman_chr6" > testRagout.txt
echo ".target = simMouse_chr6" >> testRagout.txt
echo ".hal = evolverMammals.hal" >> testRagout.txt
ragout.py -s hal -t 20 testRagout.txt

[21:42:37] INFO: Starting Ragout v2.0
[21:42:37] ERROR: "ragout-maf2synteny" native module not found
[21:42:37] ERROR: An error occured while running Ragout:
[21:42:37] ERROR: maf2synteny binary is missing, did you run 'make'?

Does anyone have a clue about what I'm doing wrong here? Or is it just a problem with the Bioconda recipe? The maf2synteny executable does indeed seem to be missing from my system.

This is what the bin directory looks like:

2to3
3EdgeTests
aa2nonred.pl
ace2sam
activate
aggregate_scores_in_intervals.py
align_print_template.py
asadmin
assistant
augustus
augustus2browser.pl
augustus2gbrowse.pl
autoAug.pl
autoAugPred.pl
autoAugTrain.pl
autopoint
autoRun.pathInfo
avro
axtChain
axt_extract_ranges.py
axt_to_fasta.py
axt_to_lav.py
axt_to_maf.py
bam2hints
bam2wig
bamtools
bamToPsl
bamToWig.py
bed_bigwig_profile.py
bed_build_windows.py
bed_complement.py
bed_count_by_interval.py
bed_count_overlapping.py
bed_coverage_by_interval.py
bed_coverage.py
bed_diff_basewise_summary.py
bed_extend_to.py
bedgraph2wig.pl
bed_intersect_basewise.py
bed_intersect.py
bed_merge_overlapping.py
bed_rand_intersect.py
bedSort
bed_subtract_basewise.py
bedToBigBed
bgzip
bigBedToBed
blast2sam.pl
blat
blat2gbrowse.pl
blat2hints.pl
block2prfl.pl
blossom5
blossom_randGraph.py
bnMapper.py
bowtie2sam.pl
bundle_image
bunzip2
bzcat
bzcmp
bzdiff
bzegrep
bzfgrep
bzgrep
bzip2
bzip2recover
bzless
bzmore
cactus
cactus2hal.py
cactus2hal-stitch.sh
cactus_addReferenceCoordinates
cactus_analyseAssembly
cactusAPITests
cactus_bar
cactus_barTests
cactus_batch_mergeChunks
cactus_blast_chunkFlowerSequences
cactus_blast_chunkSequences
cactus_blast_convertCoordinates
cactus_blast_sortAlignments
cactus_caf
cactus_calculateMappingQualities
cactus_check
cactus_convertAlignmentsToInternalNames
cactus_coverage
cactus_covered_intervals
cactus_fasta_fragments.py
cactus_fastaGenerator
cactus_fasta_softmask_intervals.py
cactus_fillAdjacencies
cactus_filterSmallFastaSequences.py
cactus_getReferenceSeq
cactus_halGenerator
cactus_halGeneratorTests
cactus_makeAlphaNumericHeaders.py
cactus_mirrorAndOrientAlignments
cactus_normalisation
cactus_phylogeny
cactus_preprocess
cactus_reference
cactus_secondaryDatabase
cactus_setup
cactus_splitAlignmentOverlaps
cactus_stripUniqueIDs
cactus_workflow_convertAlignmentCoordinates
cactus_workflow_extendFlowers
cactus_workflow_flowerStats
cactus_workflow_getFlowers
cairo-trace
captoinfo
cegma2gff.pl
cfadmin
chainMergeSort
chardetect
checkParamArchive.pl
checkUTR
cjpeg
cleanDOSfasta.pl
clear
clusterAndSplitGenes.pl
clusterGenes
cmpfillin
compare_masking.pl
compile_et
compileSpliceCands
computeFlankingRegion.pl
conda
conda-env
config_data
corelist
cpan
cpanm
cPecanAlign
cPecanEm
cPecanLastz
cPecanLastz_D
cPecanLibTests
cPecanModifyHmm
cPecanRealign
cph
cq
createAugustusJoblist.pl
c_rehash
C-Sibelia.py
csv2rdf
curl
curl-config
cwltest
cwltoil
cwltool
cwutil
cygdb
cython
cythonize
dbilogstrip
dbiprof
dbiproxy
dbTestScript
dbus-cleanup-sockets
dbus-daemon
dbus-launch
dbus-monitor
dbus-run-session
dbus-send
dbus-test-tool
dbus-update-activation-environment
dbus-uuidgen
deactivate
del_from_prfl.pl
derb
designer
div_snp_table_chr.py
djpeg
docker_test_script
doesitcache
dynamodb_dump
dynamodb_load
easy_install
elbadmin
enc2xs
encguess
envsubst
espoca
ete3
etraining
evalCGP.pl
eval_dualdecomp.pl
eval_multi_gtf.pl
exonerate2hints.pl
exoniphyDb2hints.pl
export2sam.pl
extractTranscriptEnds.pl
f2py
f2py2
f2py2.7
fastBlockSearch
faToTwoBit
fax2ps
fax2tiff
fc-cache
fc-cat
fc-conflist
fc-list
fc-match
fc-pattern
fc-query
fc-scan
fc-validate
fetch_file
filterBam
filterGenesIn_mRNAname.pl
filterGenesIn.pl
filterGenesOut_mRNAname.pl
filterGenes.pl
filterInFrameStopCodons.pl
filterMaf.pl
filter-ppx.pl
filterPSL.pl
filterShrimp.pl
filterSpliceHints.pl
findGffNamesInFasta.pl
find_in_sorted_file.py
findRegionsExclusivelyInGroup
fix_in_frame_stop_codon_genes.py
fix_joingenes_gtf.pl
fixqt4headers.pl
freetype-config
fribidi
futurize
galaxy-tool-test
gapplication
gbrowse.conf
gbrowseold2gff3.pl
gbSmallDNA2gff.pl
gdbus
gdbus-codegen
gdk-pixbuf-csource
gdk-pixbuf-pixdata
gdk-pixbuf-query-loaders
gdk-pixbuf-thumbnailer
genbrk
gencfu
gencnval
gendict
gene_fourfold_sites.py
genePredToBed
genePredToFakePsl
genePredToGtf
genrb
getAnnoFastaFromJoingenes.py
getAnnoFasta.pl
getLinesMatching.pl
get_objgraph
get_scores_in_intervals.py
getSeq
gettext
gettextize
gettext.sh
gff2gbSmallDNA.pl
gff2ps_mycustom
gff3ToGenePred
gffGetmRNA.pl
gio
gio-launch-desktop
gio-querymodules
g-ir-annotation-tool
g-ir-compiler
g-ir-generate
g-ir-inspect
g-ir-scanner
glacier
glib-compile-resources
glib-compile-schemas
glib-genmarshal
glib-gettextize
glib-mkenums
gobject-query
gp2othergp.pl
gpmetis
graphchk
gresource
gsettings
gsl-config
gsl-histogram
gsl-randist
gss-client
gst-inspect-1.0
gst-launch-1.0
gst-stats-1.0
gst-typefind-1.0
gtester
gtester-report
gtf2aa.pl
gtf2bed.pl
gtf2gff.pl
gtfToGenePred
gth2gtf.pl
gtk-builder-convert
gtk-demo
gtk-query-immodules-2.0
gtk-update-icon-cache
h2ph
h2xs
hal2assemblyHub.py
hal2chain
hal2fasta
hal2maf
hal2mafMP.py
hal2maf_split.pl
hal4dExtract
hal4dExtractTest
halAddToBranch
halAlignedExtract
halAlignmentDepth
halApiTests
halAppendCactusSubtree
halAppendSubtree
halBranchMutations
halChainTests
halCoverage
halExtract
halHdf5Tests
halIndels
halLiftover
halLiftoverTests
halLodExtract
halLodInterpolate.py
halMafTests
halMaskExtract
halRandGen
halRemoveGenome
halRenameGenomes
halRenameSequences
halReplaceGenome
halSetMetadata
halSingleCopyRegionsExtract
halSnps
halStats
halSummarizeMutations
halSynteny
halTestGen
halTreeMutations.py
halTreeNIBackground.py
halTreeNIConservation.py
halTreeNITurnover.py
halUpdateBranchLengths
halValidate
halWiggleLiftover
halWriteNucleotides
hb-ot-shape-closure
hb-shape
hb-subset
hb-view
helpMod.pm
homGeneMapping
htsfile
iconv
icu-config
icuinfo
idle
infocmp
infotocap
instance_events
instmodsh
interpolate_sam.pl
interval_count_intersections.py
interval_join.py
int_seqs_to_char_strings.py
jobTreeKill
jobTreeRun
jobTreeStats
jobTreeStatus
jobTreeTest_Dependencies.py
join_aug_pred.pl
joingenes
join_mult_hints.pl
joinPeptides.pl
jpegtran
json_pp
k5srvutil
kadmin
kccachetest
kcdirmgr
kcdirtest
kcforestmgr
kcforesttest
kcgrasstest
kchashmgr
kchashtest
kclangctest
kcpolymgr
kcpolytest
kcprototest
kcstashtest
kctreemgr
kctreetest
kcutilmgr
kcutiltest
kdestroy
kill_instance
kinit
klist
kpasswd
krb5-config
ksu
kswitch
ktremotemgr
ktremotetest
ktserver
kttimedmgr
kttimedtest
ktutil
ktutilmgr
ktutilserv
ktutiltest
kvno
launch_instance
lav_to_axt.py
lav_to_maf.py
lconvert
libnetcfg
libpng16-config
libpng-config
line_select.py
linguist
list_instances
load2sqlitedb
lp_solve
lrelease
lss3
luigi
luigid
luigi-deps
luigi-deps-tree
luigi-grep
lupdate
lz4
lz4c
lz4cat
lzcat
lzcmp
lzdiff
lzegrep
lzfgrep
lzgrep
lzless
lzma
lzmadec
lzmainfo
lzmore
lzop_build_offset_table.py
m2gmetis
maf2conswig.pl
maf2hal
maf_build_index.py
maf_chop.py
maf_chunk.py
maf_col_counts_all.py
maf_col_counts.py
maf_count.py
maf_covered_ranges.py
maf_covered_regions.py
maf_div_sites.py
maf_drop_overlapping.py
maf_extract_chrom_ranges.py
maf_extract_ranges_indexed.py
maf_extract_ranges.py
maf_filter_max_wc.py
maf_filter.py
maf_gap_frequency.py
maf_gc_content.py
maf_interval_alignibility.py
maf_limit_to_species.py
maf_mapping_word_frequency.py
maf_mask_cpg.py
maf_mean_length_ungapped_piece.py
maf_percent_columns_matching.py
maf_percent_identity.py
maf_print_chroms.py
maf_print_scores.py
maf_randomize.py
maf_region_coverage_by_src.py
maf_select.py
maf_shuffle_columns.py
maf_species_in_all_files.py
maf_split_by_src.py
maf_thread_for_species.py
maf_tile_2bit.py
maf_tile_2.py
maf_tile.py
maf_to_axt.py
maf_to_concat_fasta.py
maf_to_fasta.py
maf_to_int_seqs.py
maf_translate_chars.py
maf_truncate.py
maf_word_frequency.py
makeconv
makeMatchLists.pl
makeUtrTrainingSet.pl
maq2sam-long
maq2sam-short
maskNregions.pl
mask_quality.py
matchGraph.py
matchingAndOrderingTests
md5fa
md5sum-lite
merge_masking.pl
mMK_bitset.py
moc
mock-cwl-runner
moose-outdated
moveParameters.pl
mpmetis
msa2prfl.pl
msgattrib
msgcat
msgcmp
msgcomm
msgconv
msgen
msgexec
msgfilter
msgfmt
msggrep
msginit
msgmerge
msgunfmt
msguniq
mturk
mulled-build
mulled-build-channel
mulled-build-files
mulled-build-tool
mulled-search
multijob
mwmatching.py
my_print_defaults
mysql_config
ncursesw6-config
ndmetis
new_species.pl
ngettext
nib_chrom_intervals_to_fasta.py
nib_intervals_to_fasta.py
nib_length.py
novo2sam.pl
one_field_per_line.py
openssl
optimize_augustus.pl
opt_init_and_term_probs.pl
out_to_chain.py
package-stash-conflicts
pal2rgb
pango-list
pango-view
parseSim4Output.pl
partition_gtf2gb.pl
pasapolyA2hints.pl
pasteurize
pcre-config
pcregrep
pcretest
peptides2alternatives.pl
peptides2hints.pl
perl
perl5.26.2
perlbug
perldoc
perlivp
perlthanks
perror
phastconsDB2hints.pl
piconv
pip
pixeltool
pkgdata
pl2pm
plot-bamstats
pngfix
png-fix-itxt
pod2html
pod2man
pod2text
pod2usage
podchecker
podselect
polyA2hints.pl
ppm2tiff
prefix_lines.py
prepareAlign
pretty_table.py
prints2prfl.pl
prove
psl2sam.pl
pslCDnaFilter
pslCheck
pslMap
pslMap.pl
pslMapPostChain
pslPosTarget
pslRecalcMatch
pslToBigPsl
ptar
ptardiff
ptargrep
pyami_sendmail
pydoc
pyfasta
pylupdate5
pyrcc5
pyrsa-decrypt
pyrsa-encrypt
pyrsa-keygen
pyrsa-priv2pub
pyrsa-sign
pyrsa-verify
python
python2
python2.7
python2.7-config
python2-config
python-config
pyuic5
qcollectiongenerator
qdbus
qdbuscpp2xml
qdbusviewer
qdbusxml2cpp
qdoc
qhelpconverter
qhelpgenerator
qlalr
qmake
qml
qmleasing
qmlimportscanner
qmllint
qmlmin
qmlplugindump
qmlprofiler
qmlscene
qmltestrunner
qt.conf
qtdiag
qtpaths
qtplugininfo
qv_to_bqv.py
ragout
ragout.py
random_lines.py
randomSplit.pl
ratewig.pl
raw2tiff
rcc
rdf2dot
rdfgraphisomorphism
rdfpipe
rdfs2dot
rdjpgcom
README.autoAug
recode-sr-latin
referenceTests
reset
retroDB2hints.pl
rmRedundantHints.pl
route53
rst2html4.py
rst2html5.py
rst2html.py
rst2latex.py
rst2man.py
rst2odt_prepstyles.py
rst2odt.py
rst2pseudoxml.py
rst2s5.py
rst2xetex.py
rst2xml.py
rstpep2html.py
runAllSim4.pl
s3put
sam2vcf.pl
samMap.pl
samtools
samtools.pl
schema-salad-doc
schema-salad-tool
scipiogff2gff.pl
sclient
scriptTreeTest_Sort.py
scriptTreeTest_Wrapper2.py
scriptTreeTest_Wrapper.py
sdbadmin
seq_cache_populate.pl
setStopCodonFreqs.pl
shasum
Sibelia
sim_client
simpleFastaHeaders.pl
simplifyFastaHeaders.pl
sip
smtpd.py
snpEffAnnotate.py
soap2sam.pl
sonLib_cigarTest
sonLib_daemonize.py
sonLib_fastaCTest
sonLib_kvDatabaseTest
sonLibTests
splain
SplicedAlignment.pm
splitMfasta.pl
split_wiggle.pl
sqlite3
sqlite3_analyzer
stCafTests
stPinchesAndCactiTests
summarizeACGTcontent.pl
syncqt.pl
tabix
table_add_column.py
table_filter.py
tabs
taskadmin
tclsh
tclsh8.6
test_conda2
tfloc_summary.py
tic
tiff2bw
tiff2pdf
tiff2ps
tiff2rgba
tiffcmp
tiffcp
tiffcrop
tiffdither
tiffdump
tiffinfo
tiffmedian
tiffset
tiffsplit
toe
toil
toil-cwl-runner
_toil_mesos_executor
toil-wdl-runner
_toil_worker
tput
tqdm
transMap2hints.pl
transMapPslToGenePred
tset
ucsc_gene_table_to_intervals.py
uic
undill
uniquePeptides.pl
unlz4
unlzma
unxz
unzstd
utrgff2gbrowse.pl
utrrnaseq
uuclient
webserver-results.head
webserver-results.tail
weedMaf.pl
wgsim
wgsim_eval.pl
wheel
wig2hints.pl
wigchoose.pl
wiggle_to_array_tree.py
wiggle_to_binned_array.py
wiggle_to_chr_binned_array.py
wiggle_to_simple.py
wish
wish8.6
writeResultsPage.pl
wrjpgcom
wsdump.py
xgettext
xml2-config
xmlcatalog
xmllint
xmlpatterns
xmlpatternsvalidator
xmlwf
xslt-config
xsltproc
xsubpp
xz
xzcat
xzcmp
xzdec
xzdiff
xzegrep
xzfgrep
xzgrep
xzless
xzmore
yaml2gff.1.4.pl
zipdetails
zoom2sam.pl
zstd
zstdcat
zstdgrep
zstdless
zstdmt

[mikolmogorov]

Hi,

Ragout could not find the binary files - something must be wrong with the bioconda environment. If you installed Ragout into a separate environment, make sure it is activated. Your bin folder can't be the one from your new environment, since there are so many unrelated binaries.

I suggest to create a new clean Py2.7 environment: conda create -n py27 python=2.7, then do conda activate py27 and then conda install ragout. You can then verify if the binaries are installed by using which ragout-maf2synteny.

Mikhail

[amizeranschi]

Hi Mikhail,

Thanks for the reply. This was a problem with my PATH setup (I had a typo).

I have Ragout installed in a conda environment and cactus (with Hal) in a separate one.

After fixing the PATH and setting up PYTHONPATH to point to the right locations from the conda environments:

export PYTHONPATH=/export/home/ncit/external/a.mizeranschi/ragout_conda/anaconda/lib/python2.7/site-packages:/export/home/ncit/external/a.mizeranschi/cactus_conda/anaconda/lib/python2.7/site-packages:$PYTHONPATH

Ragout now works fine for me.