Create missing pathway files

[sammyjava]

• [ ] Arachis/ipaensis/annotations/K30076.gnm1.ann1.J37m/araip.K30076.gnm1.ann1.J37m
• [ ] Cajanus/cajan/annotations/ICPL87119.gnm2.ann1.L3ZH/cajca.ICPL87119.gnm2.ann1.L3ZH
• [ ] Cercis/canadensis/annotations/ISC453364.gnm1.ann1.HZJM/cerca.ISC453364.gnm1.ann1.HZJM
• [ ] Glycine/max/annotations/58-161.gnm1.ann1.HJ1K/glyma.58-161.gnm1.ann1.HJ1K
• [ ] Glycine/max/annotations/Amsoy.gnm1.ann1.6S5P/glyma.Amsoy.gnm1.ann1.6S5P
• [ ] Glycine/max/annotations/DongNongNo_50.gnm1.ann1.QSDB/glyma.DongNongNo_50.gnm1.ann1.QSDB
• [ ] Glycine/max/annotations/FengDiHuang.gnm1.ann1.P6HL/glyma.FengDiHuang.gnm1.ann1.P6HL
• [ ] Glycine/max/annotations/HanDouNo_5.gnm1.ann1.ZS7M/glyma.HanDouNo_5.gnm1.ann1.ZS7M
• [ ] Glycine/max/annotations/HeiHeNo_43.gnm1.ann1.PDXG/glyma.HeiHeNo_43.gnm1.ann1.PDXG
• [ ] Glycine/max/annotations/Hwangkeum.gnm1.ann1.1G4F/glyma.Hwangkeum.gnm1.ann1.1G4F
• [ ] Glycine/max/annotations/JiDouNo_17.gnm1.ann1.X5PX/glyma.JiDouNo_17.gnm1.ann1.X5PX
• [ ] Glycine/max/annotations/JinDouNo_23.gnm1.ann1.SGJW/glyma.JinDouNo_23.gnm1.ann1.SGJW
• [ ] Glycine/max/annotations/JuXuanNo_23.gnm1.ann1.H8PW/glyma.JuXuanNo_23.gnm1.ann1.H8PW
• [ ] Glycine/max/annotations/KeShanNo_1.gnm1.ann1.2YX4/glyma.KeShanNo_1.gnm1.ann1.2YX4
• [ ] Glycine/max/annotations/PI_398296.gnm1.ann1.B0XR/glyma.PI_398296.gnm1.ann1.B0XR
• [ ] Glycine/max/annotations/PI_548362.gnm1.ann1.LL84/glyma.PI_548362.gnm1.ann1.LL84
• [ ] Glycine/max/annotations/QiHuangNo_34.gnm1.ann1.WHRV/glyma.QiHuangNo_34.gnm1.ann1.WHRV
• [ ] Glycine/max/annotations/ShiShengChangYe.gnm1.ann1.VLGS/glyma.ShiShengChangYe.gnm1.ann1.VLGS
• [ ] Glycine/max/annotations/TieFengNo_18.gnm1.ann1.7GR4/glyma.TieFengNo_18.gnm1.ann1.7GR4
• [ ] Glycine/max/annotations/TieJiaSiLiHuang.gnm1.ann1.W70Z/glyma.TieJiaSiLiHuang.gnm1.ann1.W70Z
• [ ] Glycine/max/annotations/TongShanTianEDan.gnm1.ann1.56XW/glyma.TongShanTianEDan.gnm1.ann1.56XW
• [ ] Glycine/max/annotations/WanDouNo_28.gnm1.ann1.NLYP/glyma.WanDouNo_28.gnm1.ann1.NLYP
• [ ] Glycine/max/annotations/Wm82_ISU01.gnm2.ann1.FGFB/glyma.Wm82_ISU01.gnm2.ann1.FGFB
• [ ] Glycine/max/annotations/XuDouNo_1.gnm1.ann1.G2T7/glyma.XuDouNo_1.gnm1.ann1.G2T7
• [ ] Glycine/max/annotations/YuDouNo_22.gnm1.ann1.HCQ1/glyma.YuDouNo_22.gnm1.ann1.HCQ1
• [ ] Glycine/max/annotations/ZhangChunManCangJin.gnm1.ann1.7HPB/glyma.ZhangChunManCangJin.gnm1.ann1.7HPB
• [ ] Glycine/max/annotations/Zhutwinning2.gnm1.ann1.ZTTQ/glyma.Zhutwinning2.gnm1.ann1.ZTTQ
• [ ] Glycine/max/annotations/ZiHuaNo_4.gnm1.ann1.FCFQ/glyma.ZiHuaNo_4.gnm1.ann1.FCFQ
• [ ] Glycine/soja/annotations/PI_549046.gnm1.ann1.65KD/glyso.PI_549046.gnm1.ann1.65KD
• [ ] Glycine/soja/annotations/PI_562565.gnm1.ann1.1JD2/glyso.PI_562565.gnm1.ann1.1JD2
• [ ] Glycine/soja/annotations/PI_578357.gnm1.ann1.0ZKP/glyso.PI_578357.gnm1.ann1.0ZKP
• [ ] Medicago/truncatula/annotations/HM010.gnm1.ann1.WV9J/medtr.HM010.gnm1.ann1.WV9J
• [ ] Medicago/truncatula/annotations/HM022.gnm1.ann1.6C8N/medtr.HM022.gnm1.ann1.6C8N
• [ ] Medicago/truncatula/annotations/HM023.gnm1.ann1.WZN8/medtr.HM023.gnm1.ann1.WZN8
• [ ] Medicago/truncatula/annotations/HM034.gnm1.ann1.YR6S/medtr.HM034.gnm1.ann1.YR6S
• [ ] Medicago/truncatula/annotations/HM050.gnm1.ann1.GWRX/medtr.HM050.gnm1.ann1.GWRX
• [ ] Medicago/truncatula/annotations/HM056.gnm1.ann1.CHP6/medtr.HM056.gnm1.ann1.CHP6
• [ ] Medicago/truncatula/annotations/HM058.gnm1.ann1.LXPZ/medtr.HM058.gnm1.ann1.LXPZ
• [ ] Medicago/truncatula/annotations/HM060.gnm1.ann1.H41P/medtr.HM060.gnm1.ann1.H41P
• [ ] Medicago/truncatula/annotations/HM095.gnm1.ann1.55W4/medtr.HM095.gnm1.ann1.55W4
• [ ] Medicago/truncatula/annotations/HM125.gnm1.ann1.KY5W/medtr.HM125.gnm1.ann1.KY5W
• [ ] Medicago/truncatula/annotations/HM129.gnm1.ann1.7FTD/medtr.HM129.gnm1.ann1.7FTD
• [ ] Medicago/truncatula/annotations/HM185.gnm1.ann1.GB3D/medtr.HM185.gnm1.ann1.GB3D
• [ ] Medicago/truncatula/annotations/HM324.gnm1.ann1.SQH2/medtr.HM324.gnm1.ann1.SQH2
• [ ] Medicago/truncatula/annotations/R108.gnmHiC_1.ann1.Y8NH/medtr.R108.gnmHiC_1.ann1.Y8NH
• [ ] Pisum/sativum/annotations/Cameor.gnm1.ann1.7SZR/pissa.Cameor.gnm1.ann1.7SZR
• [ ] Trifolium/pratense/annotations/MilvusB.gnm2.ann1.DFgp/tripr.MilvusB.gnm2.ann1.DFgp
• [ ] Trifolium/subterraneum/annotations/Daliak.gnm2.ann1.MFKF/trisu.Daliak.gnm2.ann1.MFKF
• [ ] Vigna/radiata/annotations/VC1973A.gnm7.ann1.RWBG/vigra.VC1973A.gnm7.ann1.RWBG
• [ ] Vigna/unguiculata/annotations/IT97K-499-35.gnm1.ann2.FD7K/vigun.IT97K-499-35.gnm1.ann2.FD7K

[jd-campbell]

@adf-ncgr I just noticed this. And wonder how I can help close this issue.

[adf-ncgr]

@jd-campbell thanks, and good question. I think Sam and I had more or less decided that the pathway inference procedure was somewhat dubious anyway, but it might be worth revisiting. My vague recollection was that we were relying on gene families to project the pathways from plant reactome onto other genomes (which maybe isn't all that different from what plant reactome does to create many of their species pathway views). Anyway, the files are not strictly necessary but if we decide that doing this for every genome provides some value we can try to figure out exactly how Sam was doing this previously.